I agree that if you allocate every payroll when your document says allocate annually you could have an issue, but if we are talking about a 3% SHNE as the OP states, it shouldn't matter. If it were a match and you allocate on a payroll basis, the difference could be significant.
That said, there is a difference between allocate and deposit. Many plans allocate on an annual basis, but deposit on a payroll basis with a true-up at the end of the year. Its more of a cash flow management issue.
The FTW compliance / admin module has a true-up feature that will calculate it for you.
I don't think a mistake that misses someone here and there, which is later fixed, is a big problem. But if you only make the 3% deposit each payroll for the people who defer, and once a year for those who don't, you would have a problem.