I started the Imperial campaign today and am having issues with additional ships purchased for my Space Marine fleet. I bought an additional cruiser and it shows in the fleet screen on the campaign map, however when I enter battle it is not present for the mission itself. I have added ships to my imperial fleet and fought with them without any issues, but the space marine fleet seems to be a problem. It feels like I've wasted resources now, should definitely be something to look at fixing.
More than likely you've hit the leadership limit for the battle (big number in the middle before the mission loads)
At this point any additional ships get brought in as reinforcements if you lose any ships during the battle.
It's somewhat annoying but you're currently unable to choose the ships you want to bring in on the first wave
Same applies for the A.I.
I thought that might be the issue, however I brought in my adeptus mechanicus fleet which was in fact larger and was able to use all ships. The issue was specific to the space marine fleet. Starting a new campaign fixed the issue.
I have also seen reports of players purchasing weapons platforms and not having them appear in battle as well so I feel that this is a technical issue, not a feature.
If I am wrong (and I could be) then it should be more clear that the ship is in reserve to avoid confusion.