Can infrared electronics be harmed by an incompatible remote signal?
It would not damage them. They are designed to ignore spurious signals. While they may sometimes misinterpret bad signals, the worst that would happen is the units thinking they were sent a particular command when they weren't. So it might turn on/off when it wasn't supposed to, it might change channel, turn up/down the volume, etc. It wouldn't do any more harm than if a toddler was randomly pressing buttons on the remote.

There are various kinds of signals an IR remote might send. They are sent on a kind of carrier wave - as with radio signals. And on that carrier wave, bits are sent which represent a command. Usually these are standard commands and carriers, but not always. So this probably explains why your signals are not being interpreted - incompatible carrier, or incompatible commands. 

For more information, read Wikipedia's page on Consumer IR which gives an overview of common IR protocols.