"Penalties - It's very important that you complete Part 2 of Form 941 or Form 944, Schedule B (Form 941), or Form 945-A (if filing Form 944) correctly, or it may appear that you didn't deposit your taxes when due. There's a late deposit penalty ranging from 2% to 15% depending on the length of time the deposit is late.

Generally, unless you're eligible to pay taxes with your return, you should have deposited your taxes and shouldn't have a balance due with Form 941 and Form 944. If you pay taxes with your tax return that should have been deposited, you may be subject to a penalty. See Topic No. 757 and Publication 15 for rules on deposits and payment of tax with your return. Be sure to sign and date Form 941 or Form 944 before mailing."

What about any 1099-Misc? That is a worse penalty.