I'm fairly certain that this has to do with pitch in Japanese and accentuation in English.
The natural pitch for デバグ【HLL】 is HLL, whereas デバッグ【LHLL】 would naturally be LHL (and バグ【HL】 is HL). To mimic accentuation by pitch (i.e. accented syllables get a high pitch after transliteration), the ッ is necessary to give the バ a (natural) high pitch. バグ already has the right pitch pattern and the best pronunciation approximation to "bug".
(Besides, バッグ is already a word, although here the ッ is probably used to imitate the /æ/ sound, like in キャッシュ "cash".)
So both バグ and デバッグ are to be the expected transliterations, and either pair バッグ/デバッグ and バグ/デバグ has shortcomings, albeit being more consistent in some sense.