My Phil does things like that too. He had a Tea Tatsu facing his table like that stereo that basically ruined the look of his house. It took me a while to get him to sell it when he invited me over.
It's possible that the original house contained something like a couch and a table/cushion/etc in the layout, which is why it does that in your villagers' houses. All villagers have a particular layout of where furniture can be placed in their house.
For example, Pecan in my town has a couch and there was originally a marshmellow chair in front of it. But when Pecan started getting more furniture and shirts, the shirts will be right in front of the couch.
The only way to fix it is to give them more furniture or make them buy furniture from Retail to replace it. But I've noticed that villagers have a cycle of which item they replace next, so it might be a while unless they ask specifically that they want it replaced.