There are many script instructions that are simply math or stack manipulation that were written for versatility or future use. To eliminate potential bugs and undefined states, some non-money transfer instructions as originally implemented by Satoshi have been disabled. Transactions including them would be invalid, and modified or non-Satoshi clients including them in a block would result in an invalid "fork" block, ignored by the rest of the network.
You can see which instructions are disabled:
https://en.bitcoin.it/wiki/Script#Splice