The visitors took a 2-0 lead into half-time thanks to Adam Johnson's free-kick and a deflected finish from South Korean Ki Sung-yueng.
Fulham responded through Steve Sidwell's header but Ki teed up Johnson's second before the Sunderland-born winger converted a late penalty.
Fulham have now conceded 46 goals in 21 league matches, more than any other side, and Meulensteen said: "You just can't make progress doing that, not at all.
"We were quite in control early on and then we didn't convert those chances, from (Dimitar) Berbatov and (Adel) Taarabt.
"We gave ourselves a mountain to climb.
"These are the games you need to win; simple.
"Their third goal was the defining moment and credit to them for that.
"We've got to get conceding those goals out of our system."
- Sports & Recreation
- Steve Sidwell