first of all: i use an older traktor version (1.2.7) and the layout and command names vary from the latest version of traktor. little differences don´t have to bother you because the way to find the error is the same.
Step 1:
make sure the button/jogs are not broken.
connect the vci, start traktor. everytime you push buttons traktor receives midi signals and indicates this by lighting up a little “control” light in traktor. (the same happens on the vci, the “data” led lits up.)
try the problematic buttons, to see if traktor is receiving the signals of the button/jog!
-if the lights turn up, your vci is not broken! 
-if the control light in traktor doesn´t turn on while pressing/touch the button/jog, it´s a vci problem. 
(I don´t think it´s broke, I believe the problem is in your mapping. what mapping do you use? tried another mapping?)
Step 2:
get into the controller manager.
the keyboard mapping is selected by default. (you can´t change the position of the mappings)
click on the little triangle next to the mappings name to expand the “device” list and select the mapping for your vci!
in my setup are 7 mappings loaded for 3 different devices (keyboard, nanopad, vci100).
i don´t know what vci mapping you loaded and what its name. have a look and you will find it. select it from the list. now traktor shows the commands of the vci midi mapping.
have a look at the in-port & out-port box, it will say “vestax pc controller”. 
in the “assignment table” all midi commands from and to the vci are listed.
you can sort the commands by clicking in the header (control, I/O (input/output), mode, mapped to, ..)
here you can search for the commands (cue, play, cup,..) and look for the error.
Step 3:
locating the error.
in step 1 we excluded a vci problem.
now we have to exclude that a command in the tsi file (mapping file) is messed up.
because my command names differ from newer traktor versions, I can´t tell you which command you have to check. you need to know which function is buggy and on which modifiers it depends! this is a little bit advanced… you have to know under which conditions (modifiers) a commend should be triggered. and the best way to see a mapping as a whole is to look tutorials, read the djtt blog, experiment with own mappings and to use the manual (RTFM). 
BUT there is a fast and dirty way to find the desired commands.
Here you find a midi note layout of the vci100se (firmware 1.4!)
one picture shows the output notes (LEDs), the other one shows the input notes (command trigger signals) for traktor.
which buttons make problems? have a look which midi note makes problems! then sort the “assignemt table” by “mapped to” and scroll to the desired midi note to check if the commands are correctly triggered.
Attention: the jog wheel is sending a lot of different notes depending how it is used! AND by pressing the scratch button these midi notes change to other notes!
__
MIDI notes for the RIGHT jogs on a vci 100 (FW1.4)
-outer jog turned clockwise (without touching the metal plate) > ch2 C4
-outer jog turned against clockwise (without touching the metal plate) > ch2 C#4
scratch button on (default)
-jog tap (touching the metal plate) > ch1 B2
-jog turning (touching the metal plate) > ch2 cc017
scratch button off (LED off)
-jog tap (touching the metal plate) > ch1 F#8
-jog turning (touching the metal plate) > ch2 cc019
Hope you understand the instructions in bad english. 
Don´t hesitate to ask further questions.
But let me know what computer you use, which traktor version you run, what mapping you imported and which firmware the vci has. additionally it would be useful to know if you checked step 1 and if the problem occurs when another mapping is loaded. https://maps.djtechtools.com/