Flow through structure Mass balance Issue

Always having mass balance issues when utilising flow through structure. It could be something from adding orifice to inlets same size as pipe, lifting/dropping structure slightly increasing/decreasing length of structure, that sorts the issue. This issue only seems to exist in flow through structure. If the structure is replaced with depth/area then there is no issue but then we have to change inlet/outlet pipe lengths so they meet at the same node. Is there someway to resolve this, so the structure works as designed and we are not having to change the design just to resolve the mass balance issue.