As an independent film director, I have learned many valuable lessons within every shoot I've been involved in - Especially the productions I have been in charge of. One of the most important things, if not THE most important thing, I have learned thus far is that as an independent filmmaker you need to prepare yourself for the worst possible situation that could happen during a shoot. It is a common mistake I see time and time again from many amateurs - They don't prepare for much, and they most certainly don't plan anything.
It is vital to having a healthy production that you take the necessary amount of time and effort to determine all major conflicting situations. If your list is not a long one then keep thinking, you're nowhere near done! When you plan for problems, it will usually mean that when those problems arise they can be taken care of quickly and efficiently. It's a great way to stay on schedule and in return, also means that you'll have more time to shoot.
You should have different backup plans to resolve each and every situation. It is a lot of work but it is your job as a director (and most likely producer) to maintain a kind of control that lets people know if they have a problem they can always come to you and expect an answer that resolves their issue immediately or near immediately. It will not only make you appear more professional but it will force an amount of respect from your actors and crew members.
The worst thing a director could say to anyone on his crew is, "I don't know." Even if you really don't know, play it cool and let them know that you'll have/get an answer for them soon. With all of these things in combination you will have a production that, from an outsider's perspective, appears to flows seamlessly even though you know better.
When you've got a great list of problems along with their solutions and begin to create a schedule for your shoot, you should consider to keep those problems in mind and give room for them. If these problems never happen then you'll be ahead of schedule and EVERYONE will appreciate it. You'd be surprised how many people don't even think to do this but it really does help, and it gives a sense of freedom on set knowing that you've got time to work things out if they should ever come up.
I've seen people purposely not give room for problems in their schedule because they don't want to appear as if they aren't bulletproof. For these people I always ask, "Would you rather look like a fool and be behind schedule due to factors you knew would be there but didn't prepare properly for or would you rather be ahead of schedule and getting more work done than planned?"