I have a run which can be put in 2 categories.Its only one run but there are 2 categories in a game which I can Submit . So the question is can I submit the same run for both of the categories in that game

There is no site-wide policy for this case; different game moderators will handle it differently. So check with the moderators of the game you ran. Alternatively, you can just submit your run to both of the categories - worst case is that one will be rejected.

If it applies you can. If a mod denies it either 1.) It doesn't follow some kind of rule in one of/both of the categories 2.) They're cringe