Here's a general "bug" that pops up in several multi-ship missions like Shipyard Assault/Defense, Base Assault/Defense, Planet Assault, and Deep Space Encounter:
You never (or almost never, can't be sure it's 100% of the time) get your own race as allied AI ships, but instead get your closest allied empire's ships. Sometimes, possibly depending on political tension settings, you can even draw your enemies as allies (so you get missions where sets of same-race AIs fight each other). In short, the whole ally/enemy drafting/spawning is out of whack.
In addition, the assault/defense missions seem to not allow pirates to be drafted as allies. A pirate may draft allied empire players as allies, but not other pirates. Empire players cannot draft pirate allies.
Also, some missions have no hex defense value (DV) effect, and most do not work well when considering cartel layer ownership of hex (can hurt your own hexes with wins if cartel ownership is enemy or neutral). I don't have complete results, and my old notes are suspect. It would help if players could get on a test server or run single-player campaigns to check all possible effects. For instance, Deep Space Encounter seems to be much more reliable in boosting hex DVs in your own space when cartel ownership is enemy or neutral, but what are the hard results when tested repeatedly?
Another general problem is the planet, homeworld, and base assaults don't draft defenders (though base defense might work if fixed). Asteroid Base Assaults can be defended just fine, so it can be made to work, but does it require a new mission on the defense side for each assault script?
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Specific mission bugs:
Holding Action/Data Recovery -- Mission ends when "attacker" reaches the listening post if the enemy ships are not destroyed, but player must disengage over border if enemy ships are destroyed. It should be the other way around, so the defenders have more time to catch and kill the attacker once the data is retrieved.
Shipyard Defense -- When playing defense against the AI, smaller ships can "hide" inside the docks to trick the AI into firing on the dock more often than the player (they will sometimes shoot player during overruns). This is probably not script-fixable, but more an AI behavior problem.
Base Assaults spawn bases at random from available bases in that year, instead of spawning the specific base type (BS, BATS, or SB) placed in the hex either in the starting map or by players. Unfortunately, the script may not be able to tell what type of base is there in the database.
Planetary and Homeworld Assaults -- Homeworlds (the really nasty ones from the shiplist that are race-specific) are spawned in both types of assaults seemingly at random, when they should ONLY and ALWAYS be spawned in homeworld assaults.
Convoy Escort -- Will draft an allied player or AI of another race as enemy if they are the closest ship on the map, or have the closest base or planet on the map if no ship is in drafting range. This can cause DV effects to cancel out, since your team both wins and loses the mission.
Enigma -- The derelict patrol AI opponent will not fire on you until the derelict is destroyed or self-destructs. The mission also doesn't draft allied players, though it can draft enemies (at least 1).
Starbase Construction -- Will not draft allied players to help you defend the base, which can be very necessary when facing some of the tougher AI attacking fleets. Oddly enough, this mission CAN draft enemy players as the attackers, though it seems rare. Also, you can buy 2 bases and run one mission that will have BOTH bases spawned in the mission. If one is destroyed and one lives, I -think- you still get a base placed on the hex, but maybe not the DV boost or prestige win. This needs to be tested further.
Surprise Reversed -- Will often (always?) disregard ship release dates when determing which AIs to spawn in enemy fleet. The most obvious recurring result is the presence of X-ships in the early/mid/late eras.
Quarters/Investigation -- This mission may boost your hex DV even if you lose. Also, enemy ship is so close to border when it activates that players have to be extra careful not to accidentally disengage.
Anomaly -- The engine drain does not affect fighters, and is also too easy for drone-armed ships, since drones can still be fired and fly at all times (even if firing ship is hit by engine drain).
Super Fleet -- It's not clear this mission ever actually gets offered. It may be a Deep Space Encounter variant. There's no real indication why there would be 2 DSE missions, or why one seems not to run, unless it is flipside "defense" script only used when players are involved on both sides, like the Shipyard Assault/Defense pair.
Negotiation -- The enemy ship running for the planet is almost impossible to catch at full speed (unless you get a weakly-powered small ship). It also seems to get inside the planet range way too far out from the planet. The ship should probably spawn further away from the planet, have an activation delay, and/or need to get closer to planet for it to win. Though there is a negotiation option with text messages to choose from, it doesn't appear to affect the outcome.
Recharge -- The mission tells you to investigate the dock, but attempts to use the dock to repair generally don't work, and the mission won't end unless you disengage, usually for a loss. It also does not (or usually does not) spawn enemy ships, though enemy players MIGHT be draftable.
Salvage -- Like the recharge, enemy ships never, or almost never, get spawned/drafted. While the one is unwinnable, this one is an automatic win -- you need not do anything as long as you disengage over the border. Assuming you don't self-destruct, you will end up with a win.
Epicenter -- If facing an AI, the warship will not do anything until/unless you attack it. It does not try to save its freighters at all. It will only attack if you fire first. If facing a player, both sides can get prestige wins by saving their freighters and not engaging each other in battle (one player must disengage to end mission). This last one isn't so bad, since it offers a peaceful resolution if the combatants wish to take advantage of it.
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Again, more testing is needed, specifically on DV results and drafting/spawning.