At one level (the level of arithmetic), the loss has a really simple explanation: 67 shots vs. 46. While there were several reasons for this, the biggest was in offensive rebounds: 14 for the maroon team vs. 6 for the blue ones. That contrast is even more stark when you look at it from the point of view of missed shots recovered: Miss State missed 42 shots and got back 14 (33% of misses recovered), whereas UConn missed 26 shots and got back only 6 (23% recovery). If the two teams had taken a roughly equal number of shots, UConn would have won by 10-15 points.
In view of some of the comments here, it needs to be emphasized that the problem was not in shooting accuracy (at least regarding field goals as opposed to free throws): UConn shot 43% and Mississippi State shot 37%. UConn shot nearly 50% (7 for 15) from 3-point range, whereas Miss State was 6 for 22. Despite the mediocre free throw shooting, UConn scored 7 more points at the line than Miss state did.
The problem, quite simply, is that UConn did not get enough shots, and Miss State got too many. And the main reason for that was that UConn could not clear its defensive boards. In my opinion, that boils down quite simply to a size disadvantage.
In most games, UConn could overcome a size disadvantage with clever offense and defensive breakdowns by the opponents, but Vic Schaefer did not allow those methods to be used. With both teams playing effective defense and both teams unimpressive on offense, the inability to end Miss State's offensive possessions after 1 or even 2 shots was the difference maker.