i can't setup 3 monitors on new mac pro hdmi and thunder bult not working together what i can do

What is the resolution of the monitors and how are then connected?

See:

Mac Pro (Late 2013): Using multiple displays - Apple Support

Could be this:

Can I connect a DVI display?

Mac Pro supports DVI displays using Mini DisplayPort to DVI adapters. Use a single-link DVI adapter such as the Apple Mini DisplayPort to DVI adapter for DVI displays with a resolution up to 1920x1200. Use a Dual-Link DVI adapter such as the Apple Mini DisplayPort to Dual-Link DVI adapter for resolutions up to 2560x1600.

Mac Pro supports a total of two single-link DVI displays. If you connect a third DVI display using a passive adapter or a display via HDMI, it will cause one of the three displays to become inactive.

Can I connect more than 2 DVI or HDMI displays?

Mac Pro supports a total of two DVI or HDMI displays when connected via the built-in HDMI port or using the Apple Mini DisplayPort to DVI adapter. To connect additional DVI displays, use an active DVI adapter such as the Apple Mini DisplayPort to Dual-Link DVI adapter. You can connect up to six active adapter DVI displays. This requires a powered USB hub since Mac Pro offers four USB ports and you will need six to connect them all.