Often when you record audio using bad electronics the recording has a constant 'DC' level throughout the file. Because the ear cannot hear this you will not notice it until you attempt to edit in other audio when you can hear horrible clicks. If you think this is the problem you can run DC Offset Correction over the entire recording before you begin to edit. Another (and possibly better) way to deal with this problem is to run a high pass filter (say at 50Hz) over the recording.