Like others said, petting Pokemon is as simple as rubbing the stylus on the screen continuously. Assuming you're doing this right, it's safe to say this isn't a human error.
If it doesn't react properly, then it's either an issue with your console or game. Here's a few things to try:
- Power the game on and off.
- Try the game in a different console
- Try a different Pokemon
- Try testing your touch screen; make sure it works properly
- Try cleaning the console and the cartridge itself
Also ask yourself these questions:
- How old is the console?
- Where/when did you get the game?
- Has it worked in the past?
- Have you had any other issues?
From what you said so far, it's either an issue with the game or the console. Being able to narrow down which is the issue is a great first step to getting it to work.
LMAO this is exactly what I thought the problem might be but I didn't comment it because I thought that the chances were slim. There are certain Pokemon you can't pet, mostly Ghost types, if my memory is correct. Haunter and Ghastly are two examples, I guess it's because their bodies aren't solid. Don't know why this also applies to Shedinja, but I do remember it applying to Shedinja.
You also can't pet some ghost types (thanks ht) and shedninja can only be pet in certain parts of the body.