Am I alone in selecting the fleet I want to defend my system and then the computer just ignoring that selection and happily letting one of my construction/colony fleets and planets get massacred. Its very annoying.
Make sure the fleet you want has the star next to it (you can assign this by clicking on the fleet in the Battle Manager view), this should prioritise this fleet. I also make sure the fleet I want is also the only one dragged and dropped in the Battle Manager and make sure you do this for each battle if multiple occur in a single turn (multiple battles are displayed at the top of the screen) and you can have multiple battles per system too so make sure you go through each one to select the correct fleets.
Having said that, the wrong fleets are often used when multiple battles occur in a system with multiple fleets in it
Hmmm, seems to happen even with a single fleet attacking. Just had it happen, assigned my battle fleet to engage but instead the colonisation fleet decided it could do a better job.....it didn't!
Yeah Im doing both those things and still it ignores me. Basically the only way to guarantee it is to send the other fleets away, even then a passing fleet might pop in and get itself massacred. It is now the worse thing in a single player game. In multiplayer I find that other players suddenly find their fleets are ignoring them or that the research just stops which is even more distressing since it brings all mp games to a halt!
Once the pre-combat screen appears the fleet for each battle has to be selected manually. If there are three battles in a system the defending fleet has to be selected three times by clicking on the number of the battle (for each system) at the top of the screen (where it is also possible to select wether to resolve the battle manually or automatically for each of them by clicking on the crossed guns). This way I never had the problem the OP mentioned. Deploying them in the Battle Manager is not necessary this way (or giving them the star). But I often forget to select the defending fleet for all battles and end up with a colonization fleet to defend the system. But it's my fault, not the games fault.