You are using something like: Animation - Change (Targeted unit) flying height to 460.00 at 5.00
?
Where the 460.00 in my example is the height and the 5.00 is the amount of time it takes to ascend (in this case) to that height.
If not then that may be the issue. Mind I used "targeted unit" you may have to play around with the specifics - if the unit has its own variable, then use that variable name. If it is a triggering unit use "triggering unit". You get the idea.
Another possibility may be that your trigger isn't triggering. Either your event isn't being matched or perhaps your conditions are contrary, or not being met in order for the actions to fire.
If you have a lot of action commands firing in the trigger, then perhaps one or more of them is preventing the change height command to work.
An easy way to find an error in the actions of any trigger is to add:
Game - Display to (All players) the text: 1 fired!!! After an action - you can use as many of these as you like going down the length of the trigger changing the number as you go (or use a name, a letter - something that identifies for you each step of the trigger). After each step of the trigger a message will pop up saying '1 fired' '2 fired' '3 fired'.... on down the line.
So if only half of your trigger is firing you can see in the test mode where the trigger stops.