Hello, can you explain why did you remove the 'layer = -1' tag in the following ways:
 https://www.openstreetmap.org/way/59921601/ ; 

https://www.openstreetmap.org/way/59922780 ; 

https://www.openstreetmap.org/way/59932803 ; 

https://www.openstreetmap.org/way/135352074 ; 

Satellite shows that the waterways are below road level and thus 'layer = -1' seems valid. Since the tag removal, it is now conflicting with the roads above. If the tag removal is valid, then further corrections will be needed in the roads themselves. Kindly check and fix. 