Some of my invoices are not reflecting in the GSTR- filing even though they are present in BUSY. Why are these invoices not getting captured?

If the data on gst portal showing different as per BUSY data,then you need to check that maybe after return filled,data from BUSY has been modified or deleted or any ammnedment made on portal and in BUSY though BUSY ammnedment on portal is not available,for any ammnedments in gst reutrn,you can visit gst portal.In BUSY you can reconcile gst reports with portal data 
 And to reconcile gst reports,follow these steps 
 To do one-by-one or bulk GST reconciliation for a particular month in BUSY, you can follow these steps: 
 Step 1. Click on transactions. 
 Step 2 . GST misc utilities 
 Step 3. First download gstr json data for particular month and Select the Reconciliation option. 
 Step 4. Choose the desired month for reconciliation. 
 Step 5. If you want to reconcile one-by-one, select the transactions one at a time and reconcile them by matching the GST amounts. 
 Step 6. If you prefer bulk reconciliation, you can import the GST data for the selected month and reconcile it in one go. 
 Step 7. After reconciling the transactions, review the reconciliation report to ensure accuracy. 
 Step 8. Save the reconciliation report for future reference.