Clicking issue IN recording (not while recording)

I am having this issue getting random clicks/static in my recordings. Not just during the recording/playback process; I checked the audio files themselves so I know it's not just a system thing.
I tried tinkering with the buffer size and low latency mode, but even still these clicks won't dissappear.  It is quite frustrating. We had some great guitar and vocal takes but then I go to listen and there are random-*** clicks all over the place...
I'm using Logic X, audio device is a Focusrite 18i8 (via USB2), Macbook Pro:  8 GB 1067 MHz DDR3, 2.53 GHz Intel Core 2 Duo
Any ideas as to what could be causing the problem?

Well, that's the smallest buffer size, and it is better avoided exactly because of these kind of crackling errors (a small buffer size can also overload Logic very quickly). Try 64, 128 or 256 when recording, and 512 or 1024 when mixing (I use 128 and 1024 respectively).
Higher buffer means more latency, but also less strain on the CPU.
And it is generally not a good idea to record to your system drive, since there's also system activity going on on that disk. If it's only one or two audio tracks, it should be allright, and if your system disk an SSD, it does not matter, but otherwise I strongly recommend an external FireWire disk to record to (not USB 2).
If a higher buffer size (128 or more) doesn't get rid of the clicking, then you should also contact Focusrite.

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