PilotFish can reject messages at various levels—file (ISA/IEA), group (GS/GE), and transaction (ST/SE)—using XSLT to tailor conditions for each scenario. Examples include rejecting messages with incorrect sender/receiver IDs at the ISA level, mismatched group numbers at the GS/GE level, or missing segments at the transaction level. PilotFish configures and executes these rejections through detailed error handling routines, including EDI 999/997 responses or other customized error routing methods.