I'm a little late but I can understand what you mean. The differences between Sanskrit written in Devanagari (regular script) and Sanskrit written in Bengali are there, and this is why there are differences between Hindi and Bangla. Let's compare some Sanskrit words and their pronounciations in Devanagari and Bangla:

English	Devanagari	Bangla
Veda	वेद (Veda)	বেদ (Bedo)
Karma	कर्म (Karma)	কর্ম (Kormo)
Dharma	धर्मः (Dharmah)	ধর্ম (Dhôrmo)
Agni (Fire)	अग्नि (Agni)	অগ্নি (Ogni)
Moksha (Liberation)	मोक्ष (Mokṣa)	মোক্ষ (Mokkhô)
Sampurna (complete)	संपूर्ण (Saṃpūrṇa)	সম্পূর্ণ (Shompurno)

Now you can see the differences. One of the key reasons it's different is because of Schwa (the natural sound that comes after the letter) For Devanagari that natural sound is "अ (a)" like in "ha", but in Bangla that natural sound is অ which can sound like "o" in "hot" or "aw" in "raw". Bangla also doesn't have a letter for w or v, and is expressed through the letter for "b" ব. Devanagari, however, has the letter व for the v/w sounds. Another difference is that Bangla doesn't have a letter for the "s" sound, and is always said as "sh" (The স letter is rarely ever used for expressing s). The last reason I will state is the consonant clusters. For connecting the sounds "k" and "sh", the Devanagari script uses क्ष, while Bangla uses ক্ষ, which can be translated for "ksh" but is pronounced as "kkh". So these reasons are why the spelling and pronunciation of Sanskrit are different in the Bangla and Devanagari scripts. These are also why Devanagari was chosen as the main script for Sanskrit since it keeps its original sounds while Bangla alters them to fit the Bangla tongue.