I have noticed an error with the way that emission lines are plotted. Their amplitudes are being changed to be less than the maximum of the plot window. For example, if you have a line which has a peak flux density of 0.2 mJy, but you change the plot axis to have a maximum of 0.1 mJy, the apparent peak will be reduced to "fit" within the plot panel. Instead it should just appear truncated by the upper axis. This is confusing/misleading.
I have found this to be a problem with both an uploaded spectrum containing lines, and also with a flat spectrum where I use the ETC to add lines.