What kind of notation system? Can you post an image? I can think of at least two different interpretations (one for standard notation, one for Nashville Number System notation). And both of my guesses could be wrong, it could be something else...
In standard notation, a number inside a box could be used as a measure marker or rehearsal marker. “Let’s start it again at section 2.” Might also be denoted as a circle instead of a box, and / or, a letter instead of a number. This kind of rehearsal marker is often used in choral and band arranagements (situations where there is an an ensemble playing and behing rehearsed by a conductor).
In Nashville Number System, if there are two chords in a measure, it’s common to see them with a box around them (so you know it’s a single measure). For example a common turnaround progrsesion would be, in jazz lead sheet chord symbols:
iii vi  ii V  I
In NNS you might see, for the same progression:
[3m 6m] [2m 5] 1 (with the brackets being a box in the hand written version)
