Hey @Ketan_Kantilal_Shah ,
Thanks for posting this issue, it’s actually quite common.
The reason why this is happening is very likely due not having the Shipping Product’s Automation set with the Enable Bundling On.
To resolve this and guarantee that the order goes as 1 into Shopify (both the main product & shipping) make sure they both have the Enable Bundling Option ON as shown here:
Once you’ve sorted this out, you can do a test purchase to make sure everything is good to go.
You can also check this post here which might be useful too: Complete Troubleshooting Guide - Shopify Orders Not Syncing
If you run into any other issues whatsoever don’t hesitate in letting us know and we’ll be more than happy to help. 
Belén @Funnelish