This should be obvious. It is the responsibility of the candidate, not the funder, to ensure that materials are promptly submitted. Don't assume that application deadlines are malleable unless explicitly confirmed by staff. Assume that instructions and questions are included for specific purposes and are not arbitrary. Lack of clarity.
Proposal is too wordy or too long.
Jargon may be overused or misused. Since most recommendations are confidential, this is the area of an application over which an applicant has least control. Lack of sufficient advance planning regarding funding schedules by candidate. Applicant's proposal requests almost immediate funding with insufficient lag time. Most foundations want to fund ongoing research, not retroactive reimbursement for work already finished.