Not if you size the operations correctly.
Every yard (and railroad) has a certain capacity to switch, arrive and depart trains and run trains. In a yard, with no fast clock if it can switch 15 cars in 15 minutes, then it can switch 15 cars in 15 actual minutes. As long as you don't exceed that rate, you can set the fast clock speed to whatever you want and if won't jam anything up.
If I can handle 15 cars in 15 actual minutes and I run for an actual hour, and feed 4 trains into the yard, everything is OK. If I convert to a 3:1 fast clock where 1 hour represents 3 hours, and I feed 4 trains into the yard in 3 fast clock hours, everything will be OK. If I convert to a 6:1 fast clock where 1 actual hour represents 6 hours and I feed 4 trains into the yard in 6 fast clock hours, everything will be OK.
Where people go wrong is to increase the clock speed AND increase the train volume. If I can handle 15 cars in 15 actual minutes and I run for an actual hour, and feed 4 trains into the yard, everything is OK. If I convert to a 3:1 fast clock where 1 hour represents 3 hours, and I feed 12 trains into the yard in 3 fast clock hours, It will grind to a screeching halt.
Fast clocks can work fine, if you use them to adjust the time, but keep the workload in line with the capacity of the layout.