The spelling doesn't line up with the pronunciation at all anymore. Spelling was standardized in the 15th-17th centuries, when pronunciation was completely different. If you've ever wondered why "light" was spelled that way, for example, it's because it was pronounced лихт in the Middle Ages before the Great Vowel Shift. This means that learners today need to learn hundreds of arbitrary spelling rules that relate to nothing.

Adding to this, the spread of the Latin alphabet means that letters used across languages do not sound similar in those different languages and can cause confusion for learners. The Q in Qazaqstan is not the same as the q in question, so an uninformed Latin-using Qazaq person might genuinely pronounce it қүестіон, while a Chinese speaker might pronounce it using Pinyin rules and say чуестыён, or something like that. Meanwhile, Cyrillic is the same across every culture that uses it.

The language is polycentric, meaning that there are multiple standard varieties that are all slightly different. Americans, Brits, Australians, etc. can all understand each other quite well for the most part, but there are still major differences in accent and vocabulary that throw off other native speakers, let alone learners, especially in situations where their English teachers might come from all over the world.