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It's never explained and even the creators of the series seem to be deliberately avoiding any discussion on the point. There are a variety of completely speculative ideas floating around on the internet but there's not yet been an in-universe explanation.
We inherited Bumblebee’s speech handicap from the Transformers films:
that’s the Bumblebee that the ...
answered Apr 4 '14 at 16:41
Valorum
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In the episode "Armada", we discover that in Prime that Cybertronians multiply using Protoforms. The Protoforms were blank templates containing basic functionality, a transformation cog, and the capability of receiving a Spark; the Cybertronian equivalent of a soul. They are later given life and more advanced functionality. Starscream finds five of them ...
answered Mar 12 '13 at 18:42
System Down
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The closest conclusion I could come up with is that Bumblebee speaks in a binary-like/ morse code fashion where words are replaced with beeps and whirs in a pattern in which spells each sentence. Raf, as a computer genius, supposedly understands Bumblebee because he also understands the morse code which many humans have long forgotten over telephones and ...
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