Theoretically, they're different.
Practically, not so much.
They're different in that in Objective-C, objects can choose to not respond to messages, or forward messages on to different objects, or whatever. In languages like C, function calls are really just jumping to a certain spot in memory and executing code. There's no dynamic behavior involved.
However, in standard use cases, when you send a message to an object, the method that the message represented will usually end up being called. So about 99% of the time, sending a message will result in calling a method. As such, we often say "call a method" when we really mean "send a message". So practically, they're almost always the same, but they don't have to be.
A while ago, I waxed philosophical on this topic and blogged about it: http://davedelong.com/blog/2009/10/04/observation-objective-c
edit
To directly answer your question, there's usually nothing wrong with saying "calling a method" instead of "sending a message". However, it's important to understand that there is a very significant implementation difference.
(And as an aside, my personal preference is to say "invoke a method on an object")