IRS regulations require that commuter benefits funds designated for transit must be used to pay for transit and not parking, and vice versa. Normally, the Zenefits Card system can tell which kind of purchase you're making based on the the type of code used by the merchant or point-of-sale kiosk.
However, Caltrain's parking system doesn't differentiate between transit passes and parking passes, and uses the same transit code for both. When you try to use your Zenefits Card to pay for parking at Caltrain, the Zenefits Card system can't correctly tell which type of purchase you're making and may either decline the transaction, or incorrectly debit your transit funds instead of parking funds.
If you want to use Commuter Benefits to pay for parking at Caltrain, the easiest way to avoid issues is to pay out of pocket, then submit a claim. If you've already used your Zenefits Card to park at Caltrain and your transit funds were used, just contact Zenefits Customer Care to have the error corrected.