I’ve had multiple occurrences of this lately with programs installed as flatpaks, such as Audacity (audio editor). The updates section might list 3.5.4̀ for a program.
Whenever this happens I usually manually exclude any version downgrades and only upgrade the rest.
¿Can this happen due to security issues? ¿Or because the higher version has become incompatible with something else on my system?
This. I was also worried the first time I noticed, but seeing it happened often I just went on and updated anyway. No issues so far.