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;
You try to delete your Tweet which is orginally 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 whichs data is not fully updated yet by Twitter.
If one of these cases are the issue, we try to delete your tweet, however it might effect your Tweet count on Twitter due to their architecture.