Thrive always tracks all raw clicks that you send through your Thrive campaigns links.
What is tracked in Thrive is in fact the amount of visits hitting your campaign. Thrive is not integrated with your traffic source to somehow get the numbers reported by their system. Tracking is made to track all visits going through your Thrive campaign URL.
To audit the clicks coming in, you can go to Tracking > Click/Conversion Log and see every click that comes in. It's a very transparent log and you can provide them with log so they can investigate too, if you'd like.
It's possible that your traffic source has bot traffic that they are not displaying in their system. You could use our Geo-Redirect/Bot Filter to filter our unwanted bot traffic. You can also whitelist or blacklist traffic with this tool including areas like ISP, user agent, location, URL Parameter, referrer, IP, device, connection type, etc...
For example, if you're seeing a certain ISP or user agent string that's always appearing in the traffic that you think are bots, you can create a blacklist rule for them.
All traffic being blacklisted or not satisfying a whitelist filter will be filtered out to a separate report so as to not contaminate your "real" campaign stats. This traffic can also be filtered out to a "safe page" outside of your normal campaign rotations.
There are also 2 pre-defined filters "Known Bots" and "Known Bots Hosts/ISPs" that will automatically filter out known bots. Just having these may filter out most of your bot clicks.
With our list of possible rules, you can make your filter stronger and stronger over time as you get a clearer idea of the kind of traffic that comes in. Thrive has perfect transparency into the raw data of clicks that come in. You can analyze this and create effective rules to more and more precisely filter out the traffic you don't want.
For more information on this tool, please visit our support article here.