I cannot speak to how professional auditions work at all. Nor can I speak with universal certainty how all amateur auditions work, or how people react to them. That being said, I think my experience is sufficient enough to detect a few common threads that run through most community theatre auditions with amateur or first time actors. One of those threads is the mid-audition apology.
It is by no means exclusive to first time actors. I have occasionally been guilty of it myself. You skip a line in the script as you read, and naturally want to apologize for throwing other people off. It is very natural to both want to defend ourselves from potential embarrassment, while also showing respect for the time other people are putting into the audition.
I think, however, the best way to show respect for the audition, (and to look your best in the process) is to try to limit the things you apologize for during the actual read. Apologies to you out of the moment of the audition, and out of the character you are trying to play. It is true that we may not have a great deal of a character fleshed out for just the audition. However, what little that may have presented itself during the reading can be thrown off by saying "Sorry about that, it was my fault."
Keep going! Use the adrenaline that you most likely have coursing through you during the reading to push things beyond the little hitches. Most people you read with will not expect an instant apology for such things. I know I would not. Wait until the end of the audition, and then confess your sins.
This goes for the director as well. He is looking for presence, confidence, and creativity. He or she can more easily assess these qualities if you are acting through the whole audition, no matter how short it is. Indeed, your ability to pick up and recover from a mistake is quite an important skill when performing live, on stage. The director may even take note of how well you handle a mistake. The moments following a foul up may actually impress the director, believe it or not. But only if you do not stop and say "I'm sorry, my bad" or something equivalent.
None of this is to say, of course, that an apology is never appropriate. Nor do I mean to suggest that you will ruin your chances of getting cast if you apologize for something during an audition. You probably will not. Despite those assurances, refraining from the knee jerk apology it is still a good habit to get into. If you feel you have made a terrible mistake, and that you have been thrown totally off, simply ask if you may begin over again. In most cases, a director of an amateur show will be more than happy to allow you to do so. Otherwise, full speed ahead.