Stress to compress
When you compress or limit a signal, you trigger volume reduction – but how does volume reduction look when it's done to a huge, long bass wave? There's no simple answer, as this will always depend on your signal, your compressor, and its settings; but when a compressor clamps down on a bass wave, the result can be to flatten it out… if only a little bit.
When we flatten out a sine wave, it starts looking a bit more like a square wave – and that flattening must, by its very nature, mean that extra harmonics are created; the sine wave is distorted. In the quest for saturation (see Bass on small speakers), this might be just the effect you were looking for, but if you want as clean and true a signal as possible, solo the bass to check any audible effects for yourself, call up an analyser to compare the signals before and after.
One likely culprit behind this compression-distortion is the attack time of dynamics devices – raise the attack time for bass frequencies to see if it alleviates any distortion. Multiband compression or limiting can help you set up a slow attack time for your lowest sub bass band only, or even to leave the lowest frequencies unprocessed whatsoever.