Assuming you mean the Flameburst Tower on the Apprentice, I was able to see it attacking flying monsters that came in range. Are you able to get a video of monsters in range of the tower not being attacked? Additionally, what Skill Spheres are you using and what level are you playing on.

I am using the flamethrower uber-sphere for the apprentice, which turns the flame burst towers into flamethrower towers, and the flamethrower towers do not shoot at flying monters 

 http://steamcommunity.com/sharedfiles/filedetails/?id=809109050

Here is a link to an image of the uber sphere in game with it equiped

https://youtu.be/GzVczGRNm9c

Here is a link to a video of them working on ground enemies but not flying, and the video clearly shows that the towers can aim vertically

Gotcha. Thanks for reporting this.

Just to clarify, they aren't supposed to attack flying enemies, but the range indicator says that they do, which is the bug here.

Are they supposed to attack flying enemies? The tool tip for the sphere does not say the flamethrower cannot attack flying enemies. If it is the case it can't it should be mentioned in the tooltip, because now I am regretting buying the sphere.

By design, Flamethrowers are not intended to attack air enemies. In our upcoming patch, we are changing the range indicator of the Flamethower to reflect this! (The discussion of whether it should or shouldn't attack air enemies should be taken to the forums.)