Why is the pinyin of these two character is so weird? 話's pinyin is hua instead of wua.

化's pinyin is hua instead of fua.

We see that these two character pronounce differently when we speaks in mandarin.

Why is the pinyin of these two character is so weird?
I think you're reading Mandarin pinyin but expecting Cantonese pinyin.

Cantonese pinyin is like this:

化 Jyutping: faa3 / Yale: fa3 

话 Jyutping: waa6 / Yale: wa6


and actually it seems to fit what you were expecting!