This isn't very clear in the Anime but in the manga it's pretty clear that SSB has a major flaw:

In the Dragon Ball Super manga, the form is noted to have a major flaw in its stamina. If the form is subsequently used multiple times in a row, the user will be unable to exert even 10% of their power...

This may or may not have been a factor.

Also Trunks notes that Black is as powerful as himself in SS2 form while in base form. This is useful to note here for 2 reasons. 1 it shows that Black is stupid strong, and 2 it shows that form isn't everything. It really depends on the base powerlevel of the person fighting.

Goku for instance didn't have to go SSB to stay even with Black until after their first fight. He was essentially even with him in SS2 form in the 'current' timeline, where Trunks got his butt kicked in that form.

Finally Pablo has a point, and it can even be seen in this instance. Fighting and getting beat makes Saiyans stronger fast. Black got stronger then SSB Vegeta from one fight with Goku. Goku went Super Saiyan the first time after being pummled by Freiza. It's not unreasonable by Dragon Ball standards that Trunks getting his butt handed to him by Black also made Trunks much stronger for the very next encounter.

This isn't very clear in the Anime but in the manga it's pretty clear that SSB has a major flaw:

In the Dragon Ball Super manga, the form is noted to have a major flaw in its stamina. If the form is subsequently used multiple times in a row, the user will be unable to exert even 10% of their power...

This may or may not have been a factor.

Also Trunks notes that Black is as powerful as himself in SS2 form while in base form. This is useful to note here for 2 reasons. 1 it shows that Black is stupid strong, and 2 it shows that form isn't everything. It really depends on the base powerlevel of the person fighting.

Goku for instance didn't have to go SSB to stay even with Black until after their first fight. He was essentially even with him in SS2 form in the 'current' timeline, where Trunks got his butt kicked in that form.

Finally Pablo has a point, and it can even be seen in this instance. Fighting and getting beat makes Saiyans stronger fast. Black got stronger then SSB Vegeta from one fight with Goku. Goku went Super Saiyan the first time after being pummled by Freiza. It's not unreasonable by Dragon Ball standards that Trunks getting his butt handed to him by Black also made Trunks much stronger for the very next encounter.

Having watched the entire arc I can now say for sure:

1. Transforming into blue multiple times played a big role.
2. Keep track of the sensu beans, Trunks gets an extra one. For Saiyans in the middle of a fight a sensu bean is basically a +1 level.
3. Goku and Vegeta do generally fight on par with Black. Problem is, is that he +1's without sensu beans and he has an immortal partner. Really without Zamasu there who wasn't that strong comparatively - Goku smashes his head into the ground 10 or 12 times - but could be a shield and blinder against attacks. Black would of gone down 2 different times to either Goku, or Vegeta.
4. Rage plays a huge part in it. Vegeta gets stronger when he's pissed and thinks Trunks might be dead, Goku would of blown them both up when he hears what they did to Chichi if one of them isn't immortal, and Trunks final strength gain comes from being pissed off from being told protecting his loved ones is a 'sin'.

5. Finally, Trunks doesn't win alone, Goku started the meltdown, Vegeto continued it, and Trunks basically absorbed the power of a spirit bomb in the end to gain enough power to finally kill the crazy bugger.