Am I considered late in filing my taxes now because the mistake that is not my fault? I submitted it at 11:59pm on April 15th, only to wake up and have it rejected?

Really? 1 minute before midnight ??? Hope you have your clocks set to grenich mean time.

No, it is not late if this is your situation:

If you efiled before the deadline, did not request an extension, and your return was rejected, if you owe taxes due, you have a grace period of 5 days until April 20 to either correct things, resubmit, and successfully efile, or to print, sign, mail, and postmark the mailing on or before April 20.

If you are due a Federal refund, timing is not as critical as explained in this FAQ:

FAQ:   What if I e-filed before April 15, but my return got rejected after the deadline?

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