Do you mean you can only pick 2 upgrades when the titan is finished?  That's all you're supposed to get, plus another 2 every level up.

Or you can do it like I do and max the ability's and go 2/2/2 or 1/1/4 in the passive stats upgrades dependng on what titan it is.

Well it works for me anyway 

Then the three points was a bug. I have only seen two.

then i can get screenshot of me having three ability points kk i will be back, bu thinestly i thought it was three whenever i used TEC it was three

Same here, I have never once seen where you get three points to spend on upgrades.  someone is very mistaken in their memory.  I think you need to go back and play the TEC again. Ill guarantee you right now that you only get two points to spend.