I am currently trying to create with Visual Studio a C# application working with SQLite. I installed SQLite for my program with NuGet and three references appeared in the So
See Using Native Library Pre-Loading at https://system.data.sqlite.org/index.html/doc/trunk/www/downloads.wiki
You likely need to include the x86 and x64 folders under the the other SQLite DLL.
Edit: I've added the relevant info below in case the above link ever dies/changes.
If the development and customer machines may have different processor architectures, more than one binary package may be required. For this situation, using the native library pre-loading feature is highly recommended. It is available as of version 1.0.80.0 and enabled by default. In order to take advantage of this feature, the separate managed and interop assemblies must be used with XCOPY deployment (i.e. this feature is not supported by the mixed-mode assembly, nor when the assembly is deployed to the global assembly cache), resulting in an application deployment that looks something like this:
The string "bin" above represents the directory where the application binaries are to be deployed on the target machine. With the native library pre-loading feature enabled and the application deployment shown above, the System.Data.SQLite managed-only assembly will attempt to automatically detect the processor architecture of the current process and pre-load the appropriate native library.