Basic Rules about assemblies in Pro/MECHANICA Integrated Mode:

Solid Element Models...

Any surface that is coincident with another will be connected regardless of the assembly technique (mate, align...). Displacements (and temperatures) will be continuous across interface boundaries. If you want parts to be disconnected you need to model a gap between them.

Interference between parts is not allowed. Use Global Interference Analysis to check for parts that interfere.

Shell Element Models...

If the compression planes do not touch the parts will not be connected. Sometimes this may be fixed using the End Weld option. Other methods to avoid this include offsetting the part in the assembly such that the compression planes touch or by selecting a different surface for compression using the Pair Place option.

If the compression planes touch or intersect they will be connected.

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