Quota changes mid-period silently re-rate everything. When commission is a function of attainment, editing a quota changes every payout in that period, including ones already approved. Territory reshuffles and mid-year quota relief both do this. The plan should say whether a quota change applies from the change date or retroactively, because the engine will do whichever it is told.
A missing quota is worse than a zero quota. Attainment needs a denominator. If a rep has no quota row for the period, the calculation either fails or substitutes something, and a substituted default can produce payouts that look plausible and are wrong. Check quota coverage before running a period, not after.
Caps and floors interact with tier mode. A cap on a retroactive structure binds after the whole period has been re-rated, so the effective rate a rep sees can be much lower than the tier rate they crossed. If reps model their own plans, and enterprise reps do, expect that gap to be noticed.