Hi Magda @madzik, I struggle with this as well, and not just with scales! I realize we’re all different, so this might not fit your needs. What works for me is to first play the scale (or whatever) slowly without the metronome until I’m comfortable with it. Then I add the metronome at a much-too-slow tempo – so slow that I can’t mess it up (unless I lose my focus). Then I increase the metronome 5 to 10 bpm until I find the sweet spot where I can play comfortably and not make many mistakes. I spend a day or two there, then increase again. Worth a try???
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Magda, I tried playing this scale with a metronome for the first time last week and I made very similar observations.
I had started at 60 BPM and I was surprised how difficult it was. Just like you I was sure that I was able to play the scale faster. Quite much faster actually.
Then I noticed that my problem is not so much the constant metronome click but the slow speed. Once I had finally managed to play the scale up and down at 60 BPM three times without mistake I started experimenting and slowly increased the speed in +5 BPM or +10 BPM steps. The rule stayed the same, I had to play the scale three times up and down without mistake. What I noticed then is that it becomes much easier at somewhat higher metronome speed. My first sweet spot was 80 BPM and in the end I was able to play the scale at approx 160 BPM metronome speed reliably (one note a click) without mistake(s).
Maybe experimenting with gradually increasing the metronome speed to find your sweet spot could work for you too? 50 BPM feels excruciatingly slow, especially if you want to play each note exactly on the click.
Don’t give up. Take your time. Be forgiving with yourself. You can do it 
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I see that most people are having trouble with the dreaded METRODOME. Back in the first set of lessons Justin said we needed to keep are foot tapping when we play. Well this is a perfect time to do that. All down strumming and foot tapping would work great here. Foot tapping or Metrodome both help with rhythm, use one or both your choice.
The way I do it is half time foot tapping. But you heal down on the 1&3
Toes down on 2&4. You just rock your foot heal toe heal toe. The (ands )are when you foot is flat. And a bonus is you change chords when your heal is down so you know when to change chords.
Whatever you do just keep trying because one day it just magically just works and you don’t have problems.
Good luck to everyone