Plan document states that deferrals should be taken from bonuses. If that does not happen, how is it corrected? Are deferrals taken from next paycheck or skipped or returned from participant?

Were the bonues paid this year or last year?

this year

I successfully dealt with this exact problem using VCP. (Perhaps you could use SCP since your problem sounds more recent - mine occurred over a period of 5 years). I looked to the portion of EPCRS that deals with omitting an otherwise eligible participant and applied the same principles as to the bonus. (Appendix A, section .05). Remember that if deferrals are matched you will also have to correct for that.