yes... raw makes services send the command directly to the ircd without processing it. So the ircd receives a join message for a channel and thinks a new services client joined, whereas services have no clue about it.
As an example of what it can break: if the last user leaves services think the channel is empty whereas the ircd still sees the client that was joined with raw. Result is for example that services thinks all bans were removed whereas they haven't because there s still one user in channel according to the ircd. Then if for example the owner got banned, he can't use chanserv unban to get back in because services will think the channel doesn't exist and therefore can't contain bans...
Just one example...
The same probllem applies to all modules that are currently around that join more bots into channels.. none of the modules will make the bots leave when the last real user leaves.
and if you manage to send the right string with raw, you can even crash the ircd