Missed a quote. Ugh. Two guesses:
_MenuWaypoints = _MenuWaypoints +
[
[ ["Item", _x] ,
["Action", format["""[[%1,%2] ""%3""] execVM "''Scripts\TCIM\Waypoint.sqf'""""",
_num, call compile format ["%1Result", side player],_x]],
["Close", true] ]
]
_MenuWaypoints = _MenuWaypoints +
[
[ ["Item", _x] ,
["Action", call compile format["{[[%1,%2] '%3'] execVM "''Scripts\TCIM\Waypoint.sqf''"}",
_num, call compile format ["%1Result", side player],_x]],
["Close", true] ]
]