I have an SSIS project in VS:
Microsoft Visual Studio Professional 2015 Version 14.0.25431.01 Update 3 Microsoft .NET Framework Version 4.6.01590 SQL Server Data Tools 14.0.61116.0 Microsoft SQL Server Data Tools SQL Server Integration Services
Microsoft SQL Server Integration Services Designer Version 13.0.1601.5
Project > Properties > Configuration Properties > Deployment Target Version > TargetServerVersion = SQL Server 2016
I deployed and validated successfully on two SQL server instances, but cannot on a third.
The chief difference I see in the three instances is this:
First (success)
Microsoft SQL Server 2016 (RTM-GDR) (KB4019088) - 13.0.1742.0 (X64) Jul 5 2017 23:41:17 Copyright (c) Microsoft Corporation Developer Edition (64-bit) on Windows Server 2012 R2 Datacenter 6.3 (Build 9600: ) (Hypervisor)
Second (success)
Microsoft SQL Server 2016 (RTM-GDR) (KB4019088) - 13.0.1742.0 (X64) Jul 5 2017 23:41:17 Copyright (c) Microsoft Corporation Developer Edition (64-bit) on Windows Server 2012 Datacenter 6.2 (Build 9200: ) (Hypervisor)
Third (failed)
Microsoft SQL Server 2016 (SP1-CU5) (KB4040714) - 13.0.4451.0 (X64) Sep 5 2017 16:12:34 Copyright (c) Microsoft Corporation Enterprise Edition: Core-based Licensing (64-bit) on Windows Server 2012 R2 Datacenter 6.3 (Build 9600: ) (Hypervisor)
I have been unable to track down fixes for the errors via Google, and they seem to be the same as when I target SQL Server 2014. I can post those as an edit if necessary, but my suspicion is the Sql Server installation (perhaps an issue specific to the Enterprise edition or something otherwise missing from that install) and not my package based on the above.

The component metadata could not be upgraded to the newer version of the componentoccurs when there's compatibility issue between versions.