I suspect the problem isn't that the counter is injecting to the VFO but that you are hearing a combination of signals from both on the receiver. Certainly the counter will radiate some interference, especially if you have long connecting wires but nothing should be leaving the input connection. Also check you have a good low-impedance ground connection between the VFO and counter so you are not observing a voltage drop across the impedance of the output ground connection.
Brian.