These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
GBA version doesn't do the math right with certain large combinations of Klaxes;
GBA version misses some Klaxes when masses of same-coloured tiles meet;
NES and GBA versions drop the point-overrun bonus. In the original, Points Waves wanted you to meet a certain target during the level, and any points achieved beyond that were added to your bonus and thus counted double.
In "survive N tiles" rounds, the NES version doesn't count tiles that fall (and increase the drop meter) as "survived".