Whem I run force:source:convert to convert my source back into the Metadata API format the package.xml that it generates is incomplete or just wrong in some places. I have to manually enter the missing information in order for it to deploy bacl to the packaging server. I don't know if this is a bug or something I am doing incorrectly. Has anyone had similar issues?

I am trying to push a managed extension package to a scratch org but am running into some issues. The issues seem to be stemed around some custom objects that are owned by the package that is being extended. I have added the "extension" fields and can see that the objects are being added to the extension package but it is still erroring. I have attatched the errors below.
 

force-app/main/default/objects/inscor__Allocation__c.object-meta.xml                      Must specify a non-empty label for the CustomObject
N/A                                                                                       Field Employee__r does not exist. Check spelling. (88:13)
N/A                                                                                       referenceTo value of 'inscor__Company_Location__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Part_Master__c' does not resolve to a valid sObject type (138:13)
force-app/main/default/objects/inscor__Employee__c.object-meta.xml                        Must specify a non-empty label for the CustomObject
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Inventory_Line__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
force-app/main/default/layouts/Work_Order__c-Work Order Layout.layout-meta.xml            In field: field - no CustomField named Work_Order__c.Company_Location__c found (18:26)
force-app/main/default/layouts/Labor_Entry__c-Labor Entry Layout.layout-meta.xml          In field: field - no CustomField named Labor_Entry__c.Employee__c found (20:26)
force-app/main/default/layouts/Tool_Assignment__c-Tool Assignment Layout.layout-meta.xml  In field: field - no CustomField named Tool_Assignment__c.Employee__c found (28:26)
force-app/main/default/layouts/Work_Order_Task__c-Work Order Task Layout.layout-meta.xml  In field: field - no CustomField named Work_Order_Task__c.Assigned_To__c found (55:26)
force-app/main/default/applications/AvSight_Work_Order.app-meta.xml                       In field: tab - no CustomTab named Administration found

 

I am trying to push a managed extension package to a scratch org but am running into some issues. The issues seem to be stemed around some custom objects that are owned by the package that is being extended. I have added the "extension" fields and can see that the objects are being added to the extension package but it is still erroring. I have attatched the errors below.
 

force-app/main/default/objects/inscor__Allocation__c.object-meta.xml                      Must specify a non-empty label for the CustomObject
N/A                                                                                       Field Employee__r does not exist. Check spelling. (88:13)
N/A                                                                                       referenceTo value of 'inscor__Company_Location__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Part_Master__c' does not resolve to a valid sObject type (138:13)
force-app/main/default/objects/inscor__Employee__c.object-meta.xml                        Must specify a non-empty label for the CustomObject
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Inventory_Line__c' does not resolve to a valid sObject type (66:13)
N/A                                                                                       referenceTo value of 'inscor__Employee__c' does not resolve to a valid sObject type (66:13)
force-app/main/default/layouts/Work_Order__c-Work Order Layout.layout-meta.xml            In field: field - no CustomField named Work_Order__c.Company_Location__c found (18:26)
force-app/main/default/layouts/Labor_Entry__c-Labor Entry Layout.layout-meta.xml          In field: field - no CustomField named Labor_Entry__c.Employee__c found (20:26)
force-app/main/default/layouts/Tool_Assignment__c-Tool Assignment Layout.layout-meta.xml  In field: field - no CustomField named Tool_Assignment__c.Employee__c found (28:26)
force-app/main/default/layouts/Work_Order_Task__c-Work Order Task Layout.layout-meta.xml  In field: field - no CustomField named Work_Order_Task__c.Assigned_To__c found (55:26)
force-app/main/default/applications/AvSight_Work_Order.app-meta.xml                       In field: tab - no CustomTab named Administration found