I'd frame exactly the same computation you use as "the number of ways to pick the one player that is excluded from each University ...". Of course, I'd get the same answer...
As a quick enumeration of at least 26 different ways to make some of these teams...
Let $a, b, c, d$ represent the four players from the University of Maryland. Let $f, g, h, i$ represent the four players from the University of Vermont. Let $p, q, r, s$ represent the four players from Emory University. The question is this ungrammatical mess "If a team of 9 is to be formed with an equal number of players from each university, how many number of ways can the selection be done?" In particular, "how many number of ways" is not grammatically correct English. Nevertheless, we will represent a "selection" by who from each University is not selected (since listing the three selected players is equivalent to listing the one non-selected player from each University). \begin{align*}
afp && afq && afr && afs \\
agp && agq && agr && ags \\
ahp && ahq && ahr && ahs \\
aip && aiq && air && ais \\ \\
bfp && bfq && bfr && bfs \\
bgp && bgq && bgr && bgs \\
bhp && bhq && &&\text{+2 more} \\
&&&&\text{+4 more} \\ \\
&&&&\text{+16 more} \\ \\
&&&&\text{+16 more} \\ \\
\end{align*}