One of the basic rules of scientific injection molding is among the most frequently broken: aim for 95% to 99% filled parts at transfer. The cause may simply be misunderstanding what this means, and often times when troubleshooting a process, I have found that this basic parameter was missed in the job setup.
The key is truly knowing the difference between filled and packed. If you are setting your jobs up to be 95% to 99% packed, you are more than likely filling way too far, and, possibly unintentionally, completely filling the parts on first stage. This rule should not be based on a percentage of fully packed parts, so don't use 95% to 99% of what a full shot weighs when trying to establish the transfer position.