Although the description of the level claims that you only have one minute to finish the level, there is actually no time limit at all. You can get every ore even if you take your time.

You only have to reach the end of the level in time. Once that is done you can spend a week in it checking every corner if you want before going through the exit portal.

There are time limits for each trial level. You have to reach the end in e.g. a minute to be able to get the locked ores next to the exit portal.

Achieved 100% on the Shredder trail today. Now I think I understand what happened during the shotgun trail:

I've managed to reach the end of the shotgun level in under one minute and got the orb reward on my frist try. When I took my time on the second run and shot the cross at the end of the level, it still kind of looked like the hidden part with the orbs opened up, but this time the holes were too small to grab the reward. I didn't realize the difference because I already got the orbs.

Thanks for clarifying. :)