Ok what gives... Is this on purpose to make us waste our energy points???

When I'm close to ranking up, and have additional energy, I like to go back and forth between doing my mission, and then mousing over my rank to see how many points I need so that I don't rank-up and lose my extra energy points. When I'm at the point where doing a mission will make me rank up, and if I have extra energy points, I'll just throw all those points into the legion base, which causes the extra experience points to carry over to my next rank.

But now, seems like the programmers have done something so that when you're doing missions, and then break from it, the points needed for the next rank (when you mouse over your rank) IS NOT CURRENT. Meaning you get a false count, then do the mission and rank-up and lose your extra energy point.
Totally lame.
I think the same goes for when you uninstall and install modules. For example, I want to install my 4 drannik pwr cores. I install core number 1, then go down to core # 2 and click it only to find that I've just uninstalled it again because core #2 is now listed as being installed, thus causing extra damage because I just uninstalled it again.

just seems like these are all ways to make us use extra credits.

Just my view.

The answer to your first issue is found here: http://galaxylegion.com/forum/viewtopic.php?p=190725#p190725

Your other point about modules rearranging is an OLD issue. The modules rearrange to a degree based on condition and this sometimes causes people to uninstall/reinstall modules that they just clicked. This is why so many people are endorsing a more static ship configuration interface. Go here for a more in-depth discussion: http://galaxylegion.com/forum/viewtopic.php?f=6&t=16640