Its not so much of a bug but more of how the game is programmed / byproduct of the game dealing with how to animate a weapon that is not there and seems 100% intentional as a fix for that.
Now this is not 100% accurate since my game takes 4-5 min to log in and log out on so testing every instance is tough, but it is close for me at least, either the devs know this and cannot fix it or maybe me bringing this up will allow them to roll out a fix.
The issue that i can tell is how weapons are decided when they are animated. It appears to be handled differently between ships built and saved vs templates that have weapons assigned to them in blueprints. If the template used in a blueprint does not have a weapon actually placed on it in design the game will default to the red ball because if the design does not have a way to animate the attach rather than crashing i assume this was their work around. And this worked in early galciv3 because your only real options were to #1 use all the default ships and races which all where setup to animate or #2 use your own designs that are almost always saved with weapons on them to build.
The problem came to when modders replaced the hard coded races with their own. Most of those designs where not made within the game so they all lack weapons attached to the template so even though the game assigned weapons to them in the blueprints for some reason they do not work.
So the fix is ( i am not sure if there is a better way but this works 100% for me and it is tedious as heck). You have to change each ship one by one IN the game ship designer.
So lets for example take one of the Star Trek ship that airmaster made either off a mod or off the workshop. Almost all his ships do not have a "weapon" component on them so when assigned either through xml or within the in game race creator you get a red dot. So you go into the game having console up works to do this quick so you fastunlock and finish a shipyard and go into your designer. Now what you do is either find that design either within an existing design and "use design" or just by itself. Either way you strip it down completely of all its components either way you are basically have the empty ship then at that point you go to the equip and you add a weapon(s) where you want them, I just use the best beam weapon now please note it doesn't matter what weapon type you put on, if you use beam weapon for everything when the AI race makes the ship using the blueprint it will animate w/e weapon it is equipped with.
Now the best part about doing this is the weapons will ONLY animate from the where you put that weapon. So lets say with our star trek ship we only want the ship to shoot from one spot you just put 1 beam weapon where you want it to shoot and boom no more dozens of beams shooting at once. So it is great for endgame ships where you have like 20+ doom rays and it turns into just a spray. The ship will only animate 1 laser beam for all those shots. Or you want your kinetic ship to just shoot 5-10 shots instead of 50 at end game the amount of weapons you place determine that too so less will animate less but still do same dmg.
But be careful most ships are mirrored and it will mirror the weapon placement.
Now finally you save the design as a SHIP TEMPLATE name it something that reminds you of what you want to assign it to and then save. Now boom do all the ships you want to animate how you want them and go reassign them to the blueprint or match them up in the race creator in game and now they will animate the actual equipped weapon.
So anyways that is the fix at least in game. So far i have spent days doing 100s of ships i have downloaded over the years and so far all of them work and animate when i play against them and when i use the in game blueprint ships. If would be nice if stardock would find a way around this but i assume that since blueprints do not physically put the weapons on the template in the same way us putting them on the ship in the builder it made issues for them.