> I have trouble understanding how someone
is generally felt (if not understood) as aggressive, as in passive-aggressive. You literally say you "have trouble understanding *foo*" as if the problem was on your side but what is understood (and more often than not meant) is "how could anyone/you be so stupid to do/think/try this is beyond me".
"I have trouble understanding why you would use lib *foo* instead of lib *bar*" is very common on stackoverflow and other comp. sci. forums. Maybe people think it's a polite way to say things but it's worse because it's poison under veneer. If you want to point out you think it's stupid just say "I think it's stupid". 1/ it's stupid is better than you is stupid 2/ it's closer to what you want to express (or are people really so self-centred that someone else doing something they think is stupid breaks their brain ("trouble understanding")).
my 2ç.