Jem has been acting odd since he went to get to his pants that night. What surprised him that night in To Kill a Mockingbird?
Pohnpei is exactly right. This element of surprise with every possible interaction with Boo is what leads the reader to think it's possible that the original discussions about Boo may have been not completely true.
In Jem's 10 or 11 year-old mind, he probably had a variety of thoughts at play. He likely wondered who all knew those were his pants. We wonder what our parents really know about what we do wrong, we wonder how much they know. Then, we are careful not to lie, or if we do lie, we try to follow it carefully. If these pants were folded and mended, Jem is probably still wondering if the person responsible shared the information about the pants with Atticus, since the boys made up a lie to explain the missing pants originally.
What surprised Jem is that his pants were not left the way he expected them to be. He expected them to be just the way he had lost them. He expected them to still be tangled up in the fence since they were stuck (that's why he had to leave them).
But instead, someone had taken the pants and cared for them. That person has tried to patch the rips in the pants and has folded them and left them out for Jem to find. This freaks Jem out because it implies that maybe it was Boo Radley who did it.