Uncollected funds fees occur when the funds in an account are still on hold, meaning that the funds are unavailable for the transaction(s) being processed.
For example, a check is deposited but the funds for that check have a 3 business days hold on them before they are available to cover transactions. A transaction hits the account during the hold period, it gets paid (usually) but there is a fee for uncollected funds.
Anytime the funds being used are not available is when an uncollected funds fee will be applied.