A few points come to mind.
I assume that the Vector CANoe tool is only there for debugging. If so, the existing CAN busses should already have 120 Ohm resistors at each end of the bus, so you should not add another 120 Ohm resistor.
Bit stuffing is the addition of a bit of opposite polarity after 5 consecutive bits of the same polarity. It is dealt with at a very low level with the CAN engine inside the microcontroller. The transceiver doesn't take part in the logic of transmission.
You can get a bit stuffing error if two nodes try to send frames at the same time with the same IDs, and different data.
CAN-FD may be seen by a normal CAN receiver as having bit stuffing errors, because the timing of the data is different. If any nodes are transmitting at the wrong baud rate, that will be seen as frame errors, which may be bit stuffing errors.
Oscilloscope traces can be very revealing. During arbitration more than one node will be transmitting 0 at the same time. Frame acknowledgement results in a single bit 0 being transmitted by all the receiving nodes at the end of the frame. At these times, more than one node transmits a 0, and this will result in a larger voltage difference between CAN-L and CAN-H than when a single node is transmitting. An oscilloscope trace will show when different numbers of nodes are transmitting.
It is also possible to see the difference between the voltages produced by different nodes, especially if the transducers come from different manufacturers.
The Vector tools can only see 0 (dominant) or 1 (recessive).
The green trace is the difference between CAN-H and CAN-L. The red and yellow traces are CAN-H and CAN-L. They are offset slightly, and the actual voltages of CAN-H and CAN-L are nearly the same during recessive bits.