If a variant in your list is already in listed as a headword, or if it has already been listed elsewhere as a variant, it won't be included, and you'll get to see a list of such items.

In the case of ANALYSES, you may have repeats like this:

where the same form is a variant of the verb and the noun. Unless you have POS-tagged text there is no way for the software to determine whether the form analyses is a variant of the verb or the noun. So when lemmatising it will assume analyses belongs with the first form in the list -- here, the verb form.