Hi Sargas.
It sounds like you have a syndrome called "Doctor Who" where you are breaking the physical laws of the universe by sticking things that are bigger than you into a shoe box.
OK i havent tried loading a hangared carrier into a hangared carrier yet since i have had no real cause to operate that way. I will trial that out soon to test your bug.
With respect to the combat, depending on which screen you use to check the combat timers, you get a different result. If you are carrying ships then the local counter timer shows up lesser than if you go and check the global attack counter, which takes into account all the ships in your hold. From experience, those ships dont come into play until you hit "open fire" and then they evacuate out of cargo hold "hangar" to be part of the battle. (so long as you own or control those ships. corp member ships stay within the hold for combat grrr)
I'm also getting a warning that I cannot jump the mothership while it is docked in the mothership. The second attempt works.
Make sure you have the correct ship active while trying to jump. If you have a hangared ship (that is a mothership) active and hit "jump" you will get that error.
ok, the mothership (with two ships in hangers) is now in another system (7.6 LY away) and whenever I try to 'OPEN FIRE' at the original location, the docked ships still appear at the 'COM'...
I havent personally come up with the same problems, whether my "mothersip" or its assigned vessels start the combat first. What i normally do is initiate the combat with the mothership, have a look at the timer count, look to my hangar to see how many ships i have available to hold the combat, undock her/them as required to complete the mission and then move the mothership to another location. Rinse and repeat. Other than the counter-timer error from global to local on how long the combat will take, i havent had any real issues on ghosting. I have noticed that if you start multiple combats in same orbit and 1 of those is a nest and another is a hijack. then those combats appear separate and are conducted separate, and have separate counters to resolve. Unlike running 2 or 3 hijack counters, where you can finish them all in one foul "open fire" click.
Makes you see double sometimes when you count how many ships you have in combat while conducting multiple sytle and multiple system combats.