How can omnivores be in more than one trophic level?
I am not sure I fully understand where is your misunderstanding. I think your whole misunderstanding boils down to the representation of food chain. Actually, let's talk about food web as the name gives an intuition of what is happening that is more correct than the term food chain.

The conceptual view of the food web in a pyramid is super misleading. This is not how ecosystem work. But anyway, if one might want to make some ugly approximations and represent food web into a pyramid, then this person is totally free to represent one species twice, at two different levels. It makes sense that a species can eat things at several level in the same time. Just like you. You probably eat vegetables, salads, fruits, rice, corn, bread, etc... but also eventually fish and meat. Note also as indicated by @fileunderwater in the comments, that some species have different relationship with their ecosystem (typically eat different things) at different life stages.

Here are few examples of more or less realistic food webs. As you can see, one can roughly make category of trophic level but it is not all that clear.