I know that other writers have the similar character problem. If you ever seen those how-to-write books that specify characters types -- well, I've only heard two writers who actually found them useful, and one did because if she just went by instinct, all her characters turned out Apollonian in type. (The other writer found them useful to compare characters to, and if she could type them, she knew the characters were too simple.)
Fixing now -- especially when you realize this in revision -- is a little more tricky. There are limits on what can be done without disarraying the story. And if one reason why these two characters work together is that birds of a feather flock together -- well, their differences can't be such as to hamper their motives. Plus of course any questions of character arc.
Earlier in the process, it's easier. Even if it can disarrange the plot that you were expecting -- well, a lot of things can disarrange the plot. Assigning a few traits and finding that your character runs with them is one of the better ones. But revision can be tricky, since the chief tricks are motivations and the manner in which he does things. . . .