They shouldn't - have you verified that you don't have any MIDI assignments remaining in the mappings which may be affecting it and reading the fader movement as a MIDI command to do something to the track?
Using CDJ 2000 NXS2 with Traktor 2.11 with a Rane 2015 Mixer, new macbook Pro running Sierra.
When I use the pitch fader, it drops a million markers in the waveform in Traktor. It also creates blank spots in the stripe. Everything plays fine, but the stripe is permanently wrecked. I have to re analyze the track and redo the proper cue points to fix only to have it happen again when I use the players. Can anyone sort this for me?
Why are the players writing to Traktor in HID mode?
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They shouldn't - have you verified that you don't have any MIDI assignments remaining in the mappings which may be affecting it and reading the fader movement as a MIDI command to do something to the track?
I wouldn't even know how to check that. I strictly plugged and played. Here is a screen shot.

Unfortunately that screenshot doesn't provide much information...
Did you use the Setup Wizard when you first used the CDJs?
Open the Preferences > Controller Manager and see if you have anything other than the CDJ and Traktor default mapping shown:

your problem are the midi settings of the players, always choose midi channels in a range that are non standard for example player left ch. 9 and player right ch. 10.
Just check the setup of the players for this its no rocket science and your problem will be solved.