"When I was closing the suitcase, the body was not in it!"
Translation:Když jsem kufr zavíral, to tělo v něm nebylo!
it sets up the wrong focus on "inside" by placing the "uvnitř" at the end. you would be begging for a follow-up: "so you just put the body next to the suitcase or on top of it?"
the speaker, however, is clearly disavowing any connection with the apparent crime associated with the body found in his suitcase.
There are always more correct answers. As you can see at the top of this page, the best correct answer has no "tom" in it either, only "to".
If "tom" is used, then it must be used instead of "něm": "tělo v něm nebylo", or "tělo v tom nebylo". - that's accepted if you mean that the body wasn't in "it" - in some other "it" than the suitcase.