There were a lot more than just two instances. Heck, you don't even have to go between series to get them; for instance when the Borg were first introduced in Q Who they were said to only be interested in integrating new technology, but in just about every encounter afterwards its about assimilating cultures and people with little attention paid to technology. Voyager went from a set amount of torpedoes that could not be replicated or rebuilt...to firing them off like you'd hand out candy on Halloween.
I can go on, but suffice to say there are a lot of glaring inconsistencies and again...that's okay, it's something any long running story handled my multiple creative teams is going to encounter.