Our team is having the same issue,
Code:
[cRIO] edu.wpi.first.wpilibj.util.AllocationException: PWM channel 3 on module 4 is already allocated
[cRIO] at edu.wpi.first.wpilibj.PWM.initPWM(PWM.java:112)
[cRIO] at edu.wpi.first.wpilibj.PWM.<init>(PWM.java:141)
[cRIO] at edu.wpi.first.wpilibj.SafePWM.<init>(SafePWM.java:33)
[cRIO] at edu.wpi.first.wpilibj.Jaguar.<init>(Jaguar.java:41)
[cRIO] at edu.wpi.first.wpilibj.RobotDrive.<init>(RobotDrive.java:110)
[cRIO] at edu.wpi.first.wpilibj.templates.Team2745Robot.<init>(Team2745Robot.java:27)
[cRIO] in virtual method #11 of com.sun.squawk.Klass(bci=53)
[cRIO] at com.sun.squawk.imp.MIDletMainWrapper.main(99)
[cRIO] in virtual method #95 of com.sun.squawk.Klass(bci=25)
[cRIO] at com.sun.squawk.Isolate.run(1506)
[cRIO] at java.lang.Thread.run(231)
[cRIO] in virtual method #47 of com.sun.squawk.VMThread(bci=42)
[cRIO] in static method #3 of com.sun.squawk.VM(bci=6)