Yes, exactly. The Church has rules for good reason.
Now, I’m certainly NOT going to tell you to ignore the Communion fast. By no means.
However, I do want to caution you against going too far in the other direction; where the law becomes a thing to be observed for its own sake, rather than the reason why the Church gave the law in the first place.
The purpose of the law is that we be “empty” before receiving the Eucharist. As you probably know, the Communion fast has been shortened over time. So the 1-hour fast is not the same as (perhaps) a medical fast where one might be told to “eat or drink nothing” for 8 or 12 hours. What I’m getting at here is the the emptiness is not complete, but more symbolic—we are hardly starving ourselves by abstaining from food for just one hour. Still, the purpose of the law is a symbolic emptiness. Keep that in mind.
So here’s my take on your situation:
It appears to me that you made the effort to observe the fast. You avoided food for one hour in order to prepare yourself to receive the Bread of Life. If that one hour happened to be a minute or two short of an exact 60 minute, that does not change the fact that you made an honest and good-faith effort to keep the fast. You obviously thought about it ahead of time (or else you would not know what time you finished eating). So you didn’t ignore the law. You did your best to keep the one hour time—in other words, you did not say “I know I have 50 minutes, and I’m going to intentionally keep a 50 minute fast instead of a 1 hour one.”
And please understand, this is not about saying “keep the spirit of the law, not the letter.” No, I’m not saying that at all. I’m saying that one should keep both. Just don’t interpret the letter of the law to be so strict that a mere minute or 2 in the understanding of “an hour” causes anxiety.