Chevy S-10 98

Im the one that had the s10 chevy 98 truck that the shop screwed up the engine. They replaced the old engine with a low milage one, been driving it about 3 weeks now it has had a noise in it and seems to be getting worse? When I press on the gas to speed up
the managers says it may just be the exhaust? Does this sound right to you guys, im trying to be patient but its getting old. He reved up the engine under the hood and it sounded like a bumping(?Best I can explain it) inside the engine. Could they have not done somthing right when they switch out motors and its messing up slowly(bearings or somthing) thank you guys