Bug #1: Found this accidentally, playing a game with an NPR and I in adjacent systems. AI sent a large invasion fleet early on, then only 1-2 ships every few months, for a few years. They sent a new one through, and I was getting stuck with the 60 second "increment adjusted due to ship in firing range" bug, despite having no ship in firing range (and no message about NPRs fighting). I turned on SM mode and even looked around in designer mode, but couldn't find any combat. In fact, I made myself every race, and had no contacts in any system for any race, other than the one ship the NPR had jumped through. I was defending the jump point with 2 stations, each with 19 12 cm lasers on turrets, range 160,000 km, and 13 Particle Beams, range 200,000 km. Additionally, the stations each have 12 missile launchers with an MFC good out to about 50m km. The enemy ship moved out of beam range but I still got the 60 second increment, was the MFCs causing this? I was saving missile and did not want to fire them. EDIT: After a protracted fight, my defensive stations were destroyed in a hail of size 1 missile fire; however, I am still stuck at 60 second increments because "Increment length adjusted as a ship is within firing range."
Bug #2. While poking around trying to find the reason for Bug #1, I saw the NPR race had for every increment getting an error (it's scrolled out of the log so I don't have the exact quote) "2nd Alpha Squadron is attempting to transit Jump Point with a task group size of 7, but the highest jump rating is 5." I changed over to controlling the NPR, and split 2nd Alpha Squadron into a task group of 5 and a task group of 2 ships. I switched back to my player race, and after advancing time the NPR jumped 30 ships into my system. So the AI getting stopped from jumping the one task group through was apparently holding up its entire fleet.
Bug #3. After the enemy fleet finally transited, my 2 defense stations opened fire trying to do what they could. I only have one ECCM on each station, so I assign it to the Particle Beam Fire control when they fire, then assign it to the 12 cm lasers fire control while the Particle Beams recharge. After the first volley, when it came time to fire again I didn't see the log message that the Particle Beams fired, hit, or missed. In the F8 Combat Assignments Window, I saw the fire control on both stations no longer had any Particle Beams assigned to it. Figuring I mis-clicked, I reassigned them all back to the Fire Control. However, I still didn't see the Particle Beams shooting. Looking through the logs, I get the log message of the Particle Beam fire control targeting the enemy, within range. I see the log message "Particle Beam (x13) recharging, 5 power in capacitor, 15 power required to fire", but the only hit/miss messages are for the 12 cm lasers. On the next 15 second cycle, it does appear that the particle beams fire again.