lets see... Is it a Proto 2000? Do the instructions say to remove the fuel tank and then put the two included small screws into the holes to secure the shell to the chassis?
If yes, then put the coupler pockets in first! They are the first to hold the shell in place. Also, don't be afraid to give it a little squeeze to get it in. Then, put the little screws on.
If you have modified anything (like installed a decoder) make sure that nothing is sticking out! If any of the black plastic light caps or if a decoder is sticking up, the chassis will not fit into the shell. The chassis is built to be a big hunk of lead to make the engine as heavy as possible.