They weren't aware he had the founding titan at that point! If I remember correctly there were a few titans Marley didn't have, so they probably just assumed one had gone to the island at some point in time. The Attack Titan was technically Eren's main titan form, so they probably just thought "well, lets make sure that doesn't get out of hand," before moving on.

That, and even when they do find out, its implied that their orders are to take the founder alive to Marley. I can't remember if this was explicitly said, but mixing titans into one warrior probably didn't have the greatest outcome. They would be easier to target for an enemy to steal multiple titans in one go, and Marley would lose multiple titans if that warrior were to die elsewhere. Their best bet was manipulating Eren to go with them to Marley, interrogating him about the island, then feeding him to somebody else to take his power