Airline food is prepared in big batches, and then split between multiple trays. So if something bad got into, say, the chicken meal, it could possibly make everyone who ate that meal very sick. If both pilots get very sick at the same time, it might get very dangerous.

It's a longshot, but it's a possibility that they want to avoid no matter what. So just to be extra safe, they always eat separate meals, so that even if the chicken meal is contaminated, the beef meal, or the vegetarian meal is probably safe, for example.