The fines are not issued immediately. If a check is supposed to made every 7 days, it will not fine you on the 8th day - there is a considerable grace period. Further, the system cannot know (without larger changes) when a certain route was actually added to the schedule, nor when a plane "started flying".
If you indeed changed the schedule on let's say Feb 4th and you were fined on Feb 6th, then you definitely did not choose the maintenance option to be performed immediately. (which would relate to the other reported issue which I was not able to replicate). But for sure it will not fine you if the check become overdue only 1-3 game days ago. (won't say what the exact thresholds are, but they are very conservative to avoid false-positives)
Please let me know if spotted again, as I think this is either an user error or a one-time issue related to the upgrades that were in progress that time.