Not sure if this is a bug or confusing UI, and I haven't tested it outside 2E, so it might be present in Core RPG too. I did test with a fresh campaign and no extensions enabled though.
As some background, I've been using Fantasy Grounds for over a year and sometimes things just don't target what I think they will. Until today I never tried to sit down and figure out what was going wrong, because it was always happening in the heat of the moment mid-game.
What appears to be the case is that who you're targeting WITH seems dependent on whether you're clicking on a map token or clicking on a CT entry when doing the targeting.
Example in the GIF below.
Confusion who I'm targeting with
1. I have 4 combatants. It's Tester Guy's turn, and I've got him active both as the selected entry in the CT as well as the selected token. As I control-click on each token on the map, you can see that he targets them (arrows draw, and the CT entries show them targeted).
2. Now I control-click on each CT entry and one-by-one untarget those three creatures. Working as expected!
3. Now, on the map, I select the bugbear. In the CT, however, Tester Man is still selected.
4. I control-click on the three tokens that aren't the bugbear. You can see that the bugbear targets each of those other three actors, and the targeting lines draw appropriately.
5. I control-click on the three actors that aren't the bugbear in the CT. Instead of doing the targeting with the bugbear, it's doing the targeting with Tester Man. So instead of untargeting the bugbear's 3 targets, similar to how it worked for Tester Man in Step 2 above, what I'm actually doing is targeting those three actors with Tester Man.
6. (Not shown in gif). If I select the Bugbear in the CT (simple left-click) and make him the selected CT entry (just to be clear, didn't make it his turn though) and control-click on the other CT entries, now it does the untargeting with with the bugbear. End result is now he's got no one targeted but Tester Man has himself, the Aboleth, and the Ankheg targeted.
https://i.imgur.com/KXyU5Aj.gif
The confusion here to me is that who you're targeting WITH depends on which control you're doing the targeting on. I guess I'd expect them to stay in sync. If that was the only problem, I'd probably get it through my head to treat those as totally separate controls, except there are other bits of weirdness... the graphic effect on the map of the crosshairs for who is targeted gets really confusing when you start mixing who you're doing the targeting with.
Confusion about what the crosshairs mean
1. I've cleared all target's from above. It's Test Guy's turn and he's also selected in the CT. He targets the Aboleth via control-click on it's map token.
2. Without touching the CT or changing turns, I click the Bugbear map token and control-click on the Ankheg to make the bugbear target the Ankheg. Note that you still see crosshairs over the Aboleth that Test Guy targeted (but no line from it to Test Guy), and see a line from the Bugbear to the Ankheg. At this point, it's very hard to tell who is targeting what.
3. Select the "Test Guy" token again. You now see a line drawn from Test Guy to his target the Aboleth, but you also see crosshairs (with no line) over the Ankheg, which the bugbear (but not Test Guy) has targeted.
4. Hit the "next turn" button. Now the crosshairs over the Aboleth disappear, and all you're seeing is crosshairs over the Ankheg (with a line) because that's the bugbear's target. If you cycle turn back to Test Guy, it will only show his target. So basically there's something going wrong with the crosshair display if you do the targeting when it's not your turn, but it "corrects" once you change turns.
https://i.imgur.com/EDZUgdQ.gif
Disappearing crosshairs
Bonus: If you want to make it extra confusing, in step 2 above, have the bugbear target and then untarget the aboleth. Now there will be no crosshair over it, and when you select Test Guy in step 3, you'll see a line drawn to the Aboleth, but no target crosshair over it. Basically, the crosshairs are getting out of sync.
https://i.imgur.com/g2dixb6.gif
I'm also seeing some other weird cases sometimes but am having trouble nailing down steps to reproduce. Will post if I figure it out.
No idea what this is like on the player side of things, although I do hear a lot of "I swear I had that guy targeted!" comments come from them a lot.
TLDR for people who aren't Celestian: If you want to avoid mistargeting, making sure you always click on the guy you want to target with on the CT before targeting via CT or always clicking on their map token before targeting via map token will help the most (but not entirely remove confusion).