These ficta pitches were not really a part of the mode, but rather just decorative chromaticism.
When discussing ficta, I think it's often helpful to remember when it was typically used: ficta notes would be briefly introduced right at moments of cadential arrival, and then they would typically be immediately abandoned. (I'm simplifying here, because there were other uses of ficta, but this is the clearest.)
Imagine you're in A Aeolian—a very common mode and final for this style of music—and you have an interior cadence on D. In order to really push towards that D, the music will briefly introduce C♯, D's leading tone, to cadence on that D, and then revert to C♮ as the "true" third of the global A Aeolian.
With all of this said, identifying mode in polyphonic music (e.g., Monteverdi's madrigals) can be rather difficult, and it's not really just a question of "what notes are used"; in A Aeolian, you're going to find a lot of C♯s, F♯s, and G♯s. If you're interested in how mode is constructed in polyphonic music, check out Susan McClary's Modal Subjectivities.