OK. So we have a co-managed\hybrid environment. Are Applications at present though are all pushed from on site\on premises MECM (Config Manager). What I see though is that often those MECM pushed applications appearing in the Company Portal (as we would expect because that should show both applications pushed from on premises MECM and off premises Intune), but those on premises MECM applications not appreaing in the Software Centre (that should show applications pushed from on premises MECM but not applicarons poushed from off prenises Intune).
I addition if a sync is done on a device, often that will then show applications in the Company Portal that may not initially\qucikly show up in Company Portal (yet surely a Sync action should show\refresh applications that come from Intune not MECM ?). The Sync has no effect on what shows in Software Centre (as I would expect)