For oscilloscope, what are the differences for Glitch Capture Channel and Sample Channel?
According to the manufacturer, the MSO2000 series detects glitches, which it defines as infrequent, high frequency transients.  You have the option to filter out these transients via a feature called FilterVu, which acts as a low-pass filter.

Capturing the data yields both the filtered data (no glitches) and the unfiltered data (glitch waveform).  Both are displayed on the screen, although they are actually two waveforms overlaid on one another.  If the filter is set correctly, the Sample Channel should look like a smoothed, glitch-free version of the Glitch Capture Channel.  If it looks drastically different, you may have the low-pass filter set too high, filtering out higher-frequency parts of your actual waveform.

I expect Tektronix would have covered this in whatever product literature ships with the oscilloscope, which you may not have if purchased second-hand.