Even we do our best to reduce your tweet count down to "zero," in some cases, we can't do that due to some Twitter limitations, such as the following:
You try to delete your Tweet which is originally a retweet of some other account's, and the original tweet has been deleted by its owner.
You try to delete a retweet which the original poster (the source) account suspended, deleted, deactivated or became private.
Your tweet is on a server which data is not fully updated yet by Twitter.
If one of these cases is the issue, we try to delete your tweet; however, it might affect your Tweet count on Twitter due to their architecture.