Haven't thought about this before but why is it that some characters are counted double? I recently nuked my account and started over to add words. A couple of hundred characters later I then added 乐 lè as in happy. Fine. I today then added 乐 yuè as in music. To my surprise the counter did add 1 for this character. Is this the same for all the characters with multiply pinyin? Can't recall to have seen that before. There are literally thousands of them. I could agree that it is a different word but it is not a new character. Am I totally wrong here?

It might have been talking about seeing the definition or reading or some other part for 乐? There's no separate items for the two pronunciations, so you add/study 乐 as both lè and yuè together.

No, it where actually counting up on the known character part. But, since there where delays yesterday it might be that it actually counted up for some previous character. I where running through a bunch of chars rather fast so maybe it just where slow with showing other characters counting.