The IRS will process the 941 and the payment and send you a penalty notice, probably in a few months.
If you (your employer) has a clean record of filing and paying on time, you can ask for an abatement of the penalty, through a written response to the notice you receive.
You only get one, so make it count. They might abate the penalty but you will be stuck with the interest.
You will not lose your job over a $200 penalty, but you should expect some questions.
If this is a ind-contractor job arrangement you should eat, or offer to eat a portion or all of the penalty.
If you are an employee, the employer is responsible and I would not offer to eat any of it.
Was the 941 filed timely at least?
Also, some words of advice.
Always cross your T's and dot your I's. If someone wanted their books messed up they could do that themselves. Your attention to detail is what will set you apart from the rest.
Always print and maintain paper copies (and digital backups if possible) or all payroll reports/forms you file.
Always print confirmations of your payments so you have proof you scheduled the payment on time.
Always mail anything you send to the gov't via certified mail, and take it to the post office directly, do not leave in the box.
Anything you can do to establish a paper trail of proof to protect yourself, and your clients.
The bigger the $$$ behind the transactions, the more relevant a paper trail of proof becomes.
I have had to fight many cases with NYS and the IRS due to the USPS, or someone losing something at the IRS or NYS.
Having proof to fight my case results in a win 100% of the time. Without the proof I am at the mercy of the auditor.