When you say "comparing carts", with regards to 128KB, are you actually meaning to say "comparing ROMs?"
If so -- there have been tons of mask ROMs dumped for games which were dumped incorrectly (e.g. too large). I think the most famous fuck-up was Dragon Warrior 4, where the ROM was 1MByte in size, but in reality was only 512KB.
Otherwise, there's a bunch of games where the US releases are smaller than the Japanese releases, and have less content; Contra's such an example. However, just because there's less content doesn't mean the actual mask ROM has to be smaller.
People often forget that time constraints are a big deal in the working industry. This is speculative, but for example, Konami may have wanted to do with Top Gun what they did with Contra (US release is smaller, which additionally saved money due to use of a smaller mask ROM set), but ran out of time before the game had to be released in the states, so ended up using the same size mask ROMs in the US as they did in Japan -- yet the actual content may be smaller (e.g. wasted space).
Konami might have made a very large purchase (bulk) of mask ROMs as well. Without getting into CHR vs. PRG segregation, think of it this way: Konami buys a million 128KB mask ROMs for the US releases of games, regardless of actual game size. So, 64KB games end up getting written to 128KB ROMs and released as such. This can happen regardless of whatever else is going on -- they may have "pulled a Contra" with Top Gun (code/graphics-wise) to decrease the image, but then found out later that Konami had excess 128KB ROMs available in the states, so went with using those anyway.
We'll never "really" know, unless you yourself are actually dumping the carts themselves.

contra is a bad example since it actually HAD a different mapper though.