Just a few I'm aware of:

• sometimes they ignore redstone control
• they crash when broken, if they were connected to some of others mods pipes (fixed in buildcraft BuildCraft/BuildCraft#2199)
• in connection with chunk updates they cause huge fps drops

Tested with compiled version from the master branch and my dirty fork.

I hate to see this kind of report, I love my cables dearly. Can you give me a way to reproduce the problems?

Ok!
No need to worry! I accidentally mixed a few different issues.
One being: #1950
Other: MFR cables corrupt the machine after breaking them (not your fault)
Steps to reproduce redstone issue:

1. Disconnect cables with redstone signal.
2. Go away to unload the chunks.
3. results:
   and
   

Thank you! Would you clarify a bit on the MFR issue? I'll have a chat with skyboy if I can have a few more details.

So they don't really corrupt the machines. After breaking the cables machines behave as if they were still there. Here's the issue I opened: skyboy/MineFactoryReloaded#302 (comment)

You can also consider merging with #1762

@unpairedbracket's fix should solve this.