1st part: after freshly leveling up, perhaps, the hull points had not yet filled up?

2nd part: it reduces it's weapon damage and drains it's own AM with each shot it performs with each shot having a low chance of taking over an enemy frigate.

That's what I keep hearing.  It sounds like the AM usage (given that the thing has half a dozen weapon banks) is absurd and can drain your AM far too fast.

Subjugatign Assault has a number of problems.  Despite being a really interesting idea the implementation was rather poor. the cheif issues are:

1). Too much of an AM hog.  As people have said, until the titan gets to higher levels this ability will run it out of AM in no time flat.

2).  Unreliable.  Sometimes you steal 2 ships almost instantly, other times the coronata spends AM & reduces it's damage in vane, attacking for 20-30 seconds with no conversions.  This unreliability is especially an issue being that the ability has such major downsides(reduced damage & high AM consumption)

3).  The ability literally does nothing if the enemy doesn't bring frigates along(besides maybe carriers safely parked on the far side of the gravity well, ready to jump out if coronata comes their way).  This is especially annoying being that not using many frigates is a popular strategy in general for fear of feeding enemy titans.  When an opponent does choose to employ no frigates(save perhaps the aforementioned cowardly carriers), the coronata suddenly has one of it's abilities do nothing(no other titan has this issue).  Subjugating assault really need so add some sort of secondary effect when coronata attacks capital ships or titans(perhaps an AM drain?)

4).  This one is minor,  but because of the unreliability discussed in issue 2, combined with the fact that coronata's attacks do deal substantial damage as far as frigates are concerned, often times the frigates you do steal are practically dead.

Honestly this ability needs some attention.  #1 & #3 definitely need to be addressed.   #2 would be nice, and #4 is IMO the least pressing issue.  But all of these issues combined really make what should be a very interesting ability rather underwhelming.

Besides, the coronata certainly has room for some improvement, the common opinion seems to be that it is currently the weakest titan.

why does it have to drain AM at all? You've already traded dps for a chance at capturing ships. I've left the thing on and never captured anything. I don't see how it's any worse than a couple of lvl 6 raptures running around.

That sounds good.  It would no longer function if your AM got below that point and above it, provided your capture one, your AM is drained. 

Why did you make a thread and then ask the same thing again here? Yes it works you've just been clicking a toggle button repeatedly which means it does bugger all unless you switched it to ON by accident.