Use Library functions in interrupt

Hello,
In my Teensy 3.2 Project is an CAN_Write() in an 1ms Interrupt program. The "Loop()" section should poll the CANBus with CAN_Read(). 
Interruptprogram works fine all the time. The CAN_Read() works only for some seconds, then no Message from the Bus is detected.
My question: Is the FlecCAN Libary designed for Interrupt use ? Any idea how to fix the problem ?

best regards Andreas