Looks like a classic 3D problem in AC where it will where possible visually merge abutting elements if the face materials are the same. The typical workaround to prevent this is to duplicate your face material, give it a new name e.g. mat1_copy and override the face material of one of the beams with the new material. You can end up with multiple duplicates depending on the complexity of your connections but usually four variants is enough for most situations.
The other situation in plan is similar and can be overcome by changing the layer intersection number to 0 (zero) to prevent intersections.
Apple iMac Intel i9 / macOS Sonoma / AC27UKI (most recent builds.. if they work)