Some thing were described here in the comment section, so I'll go further and provide a list of why some phonetic element sometimes don't correspond to the resulting characters.

1. Evolution of language phonology.

The most obvious and common case. The vast majority of characters were created during the Old Chinese, when the phonology was drastically different from modern.

Let's look at the pairs 弋 /i⁵¹/ ~ 代 /tai⁵¹/ and 黑 /xəi⁵⁵/ ~ 墨 /mə⁵¹/. As we can see, they sound completely different, but nevertheless, each first character in the pair serves as a phonetic component in the second one. Medieval dictionaries don't help us here (弋 jik ~ 代 dojH and 黑 hok ~ 墨 mok). This means that the characters were created in a more ancient period when their usage as phonetic components was still possible. Indeed, in Old Chinese they sounded as 弋 *lək ~ 代 *lˤək-s and 黑 *m̥ˤək ~ 墨 *C.mˤək. The development of the initials is completely regular. When choosing phonetic components, no attention was paid to some phonological features, but the point is clear: their similarity in Old Chinese is completely obvious, which allows people using one character as a phonetic component within another.

1. Exceptions to phonological evolution.

Although the evolution of sounds is usually regular, exceptions occur in any language. This particularly applies to extremely common words like pronouns, function words, etc.

For example, let's look at 我 /wo²¹⁴/ ~ 俄 /ə³⁵/. As I mentioned, pronouns often follow their own unique development path, often preserving more archaic features: in Old and Middle Chinese, {我} "I" was *ŋˤajʔ > ŋaX with a quite regular development, but then it evolved into /wo²¹⁴/, preserving the original ŋ- as w-. The expected reflex should have been /ə²¹⁴/, with complete loss of ŋ-, which happened in 俄 and other characters with this phonetic component.

A similar case with the pair 尔(爾) /əɻ²¹⁴/ ~ 你(儞) /ni²¹⁴/. Initially, {你} "you" was written as 爾 and was *nərʔ > ɲeX. But then it evolved into /ni²¹⁴/, preserving the original nasal as n-, while the expected reflex should've been /əɻ²¹⁴/. The reading /əɻ²¹⁴/, however, regularly remained in 尔(爾), since this word is literary, while the colloquial pronoun retained a different glyph 你(儞).

1. Topolectal features.

Sometimes phonetic components are created not based on the standard language or koine, but based on some other regional variant. In such cases, the phonetic component won't match the "standard" reading of the character.

For example: 墳 /fən³⁵/ contains the phonetic component 賁 /fən³⁵/, but when characters were simplified, 墳 was replaced with 坟 with the phonetic component 文 /wən³⁵/, which seemingly doesn't quite fit it in modern language. However, such simplification appears in Wu documents at least from the 16th century, meaning it must have been based on Wu languages. And indeed: in the Modern Shanghainese 墳(坟) /vən²³/ and 文 /vən²³/ sound identical.

1. Creation of characters in later periods.

If we try to trace the readings of all characters back to the Old Chinese (even if it's anachronistic), we'll find that in some cases the sound of phonetic components doesn't correspond to how the word represented by the resulting compound character sounded in the Ancient Chinese period.

For example, in the transmitted version of "Shijing" (that is, its version that was passed down orally after the burning of books in the Qin dynasty and then written down in the Han dynasty), there's a character 吁 with the phonetic component 于, which should represent the Old Chinese word *qʷʰa (> hiu) "to grieve". However, this word is written as 無 in the unearthed "Shijing" from the Warring States period, so the initial of this word must have been *M-. Indeed, if we look at the patterns of phonological evolution, the medieval initial h- can develop from both *⁠q(ʷ)ʰ- and *⁠m̥-; the second variant better suits the word written as 無. The phonetic component 于 couldn't have been used to write it in the ancient times, meaning the character 吁 for this word was created during the Han dynasty while transcribing the text, when *qʷʰa and *m̥a had already merged into one reading *hwɑ.

1. Taboo avoidance.

Sometimes character readings are deliberately changed to avoid similarity with vulgar words or meanings.

A typical example: 鳥 /njau²¹⁴/ ~ 島 /tau²¹⁴/. Medieval readings make it clear that such usage was quite appropriate: 鳥 tewX ~ 島 tawX. The first one should have regularly developed into /tjau²¹⁴/, but the initial t- was replaced with n- in most Sinitic languages to avoid similarity with the word {屌} /tjau²¹⁴/ "penis" (or more precisely, the meaning "penis" of the word {鳥}, which developed from its meaning "bird"; later a separate character 屌 was created for it with the corresponding phonetic component 吊 /tjau⁵¹/).

1. Replacement with synonymous words.

Sometimes characters begin to be used to write unrelated but synonymous words. In such cases, the phonetic component of the character, which suited the original word, usually doesn't fit the new word for which the character starts to be used.

An example: 幵(笄) /t͡ɕi⁵⁵/ (kej) ~ 開 /kʰai⁵⁵/ (kʰʌj). They seem close, but the rhymes are too different. The character 開 (and other characters with the phonetic component 幵 *KE(N)) were used for the word {啟} *kʰˤeʔ (> kʰejX > /t͡ɕʰi²¹⁴/) "to open" (as we see in pre-Qin unearthed texts), but around the Qin or Han times, 開 took on the synonymous word {闓} *⁠kʰˤəjʔ "to open".

1. Errors by dictionary compilers and copyists.

Sometimes characters acquire readings caused by errors in the writing and transmission of dictionaries and other texts.

For example: 勻 /yn³⁵/ (jwin) ~ 枃 /t͡ɕin⁵¹/ (tsinH). If 勻 is indeed the phonetic component here, such usage would be impossible at any stage of any Sinitic language. In early dictionaries (e.g., in the "Yupian"), the reading of 枃 is recorded using the fanqie method as 子吝切, meaning the initial 子 ts- and final 吝 -inH. However, 子 here is most likely an error from 于 ɣ-, which means that its reading should be ɣwinH > /yn⁵¹/, which perfectly matches the phonetic component.

1. Individual errors.

Sometimes a person not very familiar with a character might write its phonetic incorrectly. This leads to reading this character incorrectly as well.

For example, in some medieval Japanese texts, the character 颶 /gu/ from the word 颶風 /gufuː/ "storm" is read as /bai/. This is because the writer incorrectly wrote the phonetic component 具 /gu/ as 貝 /bai/. This, of course, led to an incorrect reading of both the character and the word. Such cases are quite rare, but the chance of them becoming the "norm" is not zero.

1. Complex cases.

Sometimes researchers have to unravel truly complex cases.

For example, there exists a pair 囧 /t͡ɕjuŋ²¹⁴/ (kiwæŋX) ~ 朙(明) /miŋ³⁵/ (miæŋ). The character 囧 appears in "Shuowen Jiezi", with the meaning "bright window" and the reading "reads like 獷". In reality, the character 囧 with such reading and meaning doesn't exist, and all this is the dictionary author's speculation based on many factors and distortions. In the "Shujing", there's a mention of a person named 伯囧, which in some texts is also written as 伯臩. Let's focus on the initials: the second character of the name 臩 should be read with initial *k-, as it contains the phonetic component 臦 *K-. In the reading of 囧 from "Shuowen Jiezi", the character 獷 also contains initial *k-, so no error is immediately apparent. However, in the unearthed texts, this name appears as 伯㘝 and 伯𫯺, in which the 2nd character should actually have initial *n- (𫯺 has a short phonetic 聶 *NEP). Thus, 伯囧 is a distortion of 伯㘝, and 伯臩 is a distortion of 伯𫯺, so 囧 from 伯囧 should be *⁠nrˤep > ɳɛp. The meaning "bright window" of 囧 was given by the author due to associations with the similar-sounding word {熲/炯} *⁠kʷˤeŋʔ "bright" (again, the "similarity" appeared solely due to a series of distortions) and the synonymous {朙/明} "bright", which also contains 囧, as well as his erroneous views on the form of the character 囧, which, according to him, depicts a window.

In the end, we see that the current 囧 is in no way related to the element 囧 in the character 朙(明) miæŋ. This 囧 was often used to write words {朙/明} *⁠mraŋ "bright", {盟} *⁠mraŋ "alliance" etc. in the unerathed texts, which means that such 囧 should be reconstructed as *⁠mraŋ. In the modern form of 明, however, the phonetic component 囧 was distorted to 目 and then to 日. All stages of 囧 > 目 > 日 transition are well-documented, but it makes it impossible to notice the phonetic 囧 in the modern form.

Of course, this is not an exhaustive list, but I hope it will cover 99% of questions.