Not exactly a reason not to use VTP pruning but just a few attention points:
If running version 1, transparent mode will disable forwarding of VTP packets, hence making all downstream switches outside of your VTP domain and unaware of VLANs.
If you're running version 2, a switch in transparent mode will forward every VTP packet if the switch is set to NULL domain. If the domain name on the switch is set, it will forward packets only for this domain.
Most importantly: be really cautious about used equipment! When you use the "write erase" command to wipe your new-used equipment, it doesn't erase VLAN information, then if you plug it in your network and start to configure VTP, bad things might happen. If it had a bigger revision number than you have on your network, its VLAN information will now be flooded to all your switches. This will happen even if set to null domain, because when in server or client mode, the first non-null domain packet that arrives determine the new VTP domain and then it will flood its VLANs and disrupt your network.
But I would say it's a really good protocol which will save you some time if used wisely.
Edit: sorry. I misread this question as regarding VTP and not only VTP pruning and I'm not able to delete my answer :(