I notice in Career mode, my respect lowers each mission. I checked the manual, and it claimed it was for "dumb calls". I have tried my best to only use the calls correctly, so I'm puzzled. I've even had my guys use the two entry approach, lock pick things myself, throw my own cs, ect. I'm really not sure why this is happening. Anyone know?

The game doesnt seem to work properly on here. Its because when you want to report a suspect as neutralised the option isnt given to you so you have to report them as down. Your team then corrects the control room for you and this lowers your score.

Does this work properly with the retail version?

Well no, you don't have to make an incorrect report.

If your team has already reported a suspect neutralised, then that's been taken care of.

My experience is that when a team member kills someone, they report it immediately (you should definitely be able to hear them doing this), but for 'down' (i.e. still alive) suspects, it's up to you to report them, check for weapons, and request evac.

If you kill someone, OTOH, you can (and should) report them as neutralised yourself.