Possible FAFSA mistake

Pell is an “entitlement” based on EFC, not on based on “if they qualify for aid”. A student can qualify for many other types of aid without being eligible for Pell, for example merit aid or scholarships based on major (at some schools). It’s also why some schools ask for a CSS profile in addition to a FAFSA. You assume, based only on the OP asking about their status as independent, that they are eligible for Pell but you haven’t seen their actual data, if they have already reached the 8 term limit for Pell or if there are other factors that might disqualify them.