c. 1400, "hesitation, uncertainty," from Latin vacillationem (nominative vacillatio) "a reeling, wavering," noun of action from past-participle stem of vacillare "sway to and fro, waver, hesitate, be untrustworthy," of uncertain origin. Originally in reference to opinion or conduct; literal sense is recorded from 1630s.
mid-15c., from Old French fluctuacion (12c.) or directly from Latin fluctuationem (nominative fluctuatio) "a wavering, vacillation," noun of action from past-participle stem of fluctuare "to undulate, to move in waves," from fluctus "a wave, billow, surge, a flowing," from past participle of fluere "to flow" (see fluent).
"long, narrow ulcer," late 14c., from Latin fistula "a pipe; ulcer," which is of uncertain origin. Related: Fistular; fistulous (Latin fistulosus "full of holes; tubular").
No certain etymology. The best comparison seems to be with festuca "stalk, straw" and maybe ferula "giant fennel" (if from *fesula): the forms of a "pipe" and a "stalk" are similar. The vacillation between fest- and fist- occurs within festuca itself, and might be dialectal, or allophonic within Latin. [de Vaan]