Hi Jan,
I've now looked at the whole junction layout and there are anomalies, I'll try to explain the logic I assume.

The 4 sections of ref N44, (Way: Leidsestraatweg (7471615), Way: Rijksstraatweg (1216487071), Way: Leidsestraatweg (59002595) and Way: Rijksstraatweg (7471605), are the bottom layer, I've changed from layer=-1 to layer= 0, no tag as this is implied in the absence of the layer tag.

Way: 860437191, Way: 964339476, Way: 964339481, Way: Zijdeweg (860477018), Way: Zijdeweg (860437189), Way: 964339486 and Way: Zijdeweg (860437193) are all correctly tagged as layer=1 (above the N44 way sections mentioned above).

The bridge sections, Way: 328255383,  Way: Landscheidingsweg (127838915) and Way: Landscheidingsweg (127838916), are above everything mentioned in the two paragraphs above. I've changed these ways from layer=1 to layer=2.

Could you please review the changes? In case I've made a mistake the changeset is here:- https://www.openstreetmap.org/changeset/173744079

Regards Bernard.