It sounds to me like 1) your original manuscript was rejected, 2) you tried to resubmit anyways, and 3) the journal rejected your resubmission without further consideration.
The result (3) sounds completely normal to me given (1) + (2); the place where something went wrong is when you tried to resubmit a rejected manuscript. Doing so likely seems rude to the editor, though I don't think this was your intent. It's like you asked if someone would have lunch with you, they said "no, sorry, I'm busy", and then you arrived at their office anyway with sandwiches. Maybe you thought that bringing sandwiches would fix things - after all, if someone is busy, wouldn't it be useful if someone else made them lunch? However, the message they gave was really just "No", despite the extra words used.
The editor may share some blame here, because their reasons for rejection were not particularly clear and persuasive. It would have been better that they just say "reject" was the final decision and not make up reasons about timelines to revise. I suspect that they saw far deeper problems in your manuscript than you are appreciating, and that the changes you made are comparatively superficial. Importantly, you are resubmitting to the editor, not this other reviewer, so addressing the reviewer's concerns may not be sufficient. I think there is an implied statement in the rejection that is missing:
I think the manuscript can be improved and should be resubmitted (somewhere else)
I suppose if you are uncertain, you could write the editor and ask them what has happened, but I suspect all they will do is confirm that your manuscript was rejected and that this means "do not submit a revision here".
The next step is to submit the latest version of the manuscript to a different journal.