I hit the same problem when trying to add the new Numerics package to my project which contains an iOS Target called CreativeCoding, and a Mac command line target called mandelbrot.
I added the package the normal way in Xcode to the first target. I then quit Xcode and opened up the project.pbxproj file in an editor (vi of course).
I then went down to the / Begin PBXNativeTarget section / comment, found my CreativeCoding target and copied the 3 lines from the packageProductDependencies  container with the new Numerics packages (Numerics, ComplexModule, RealModule) and pasted them into the packageProductDependencies container of my mandelbrot command line target.
/* Begin PBXNativeTarget section */
            8B083F4B24F0B40000A225C8 /* CreativeCoding */ = {
                    isa = PBXNativeTarget;
                    buildConfigurationList = 8B083F6024F0B40200A225C8 /* Build configuration list for PBXNativeTarget "CreativeCoding" */;
                    buildPhases = (
                            8B083F4824F0B40000A225C8 /* Sources */,
                            8B083F4924F0B40000A225C8 /* Frameworks */,
                            8B083F4A24F0B40000A225C8 /* Resources */,
                    );
                    buildRules = (
                    );
                    dependencies = (
                    );
                    name = CreativeCoding;
                    packageProductDependencies = (
                            8B22BD29263E328B00867530 /* ComplexModule */,
                            8B22BD2B263E328B00867530 /* RealModule */,
                            8B22BD2D263E328B00867530 /* Numerics */,
                    );
                    productName = CreativeCoding;
                    productReference = 8B083F4C24F0B40000A225C8 /* CreativeCoding.app */;
                    productType = "com.apple.product-type.application";
            };
            8BE83F4F26213D1C00663AC9 /* mandelbrot */ = {
                    isa = PBXNativeTarget;
                    buildConfigurationList = 8BE83F5626213D1D00663AC9 /* Build configuration list for PBXNativeTarget "mandelbrot" */;
                    buildPhases = (
                            8BE83F4C26213D1C00663AC9 /* Sources */,
                            8BE83F4D26213D1C00663AC9 /* Frameworks */,
                            8BE83F4E26213D1C00663AC9 /* CopyFiles */,
                    );
                    buildRules = (
                    );
                    dependencies = (
                    );
                    name = mandelbrot;
                    packageProductDependencies = (
                            8BB120942622CCB8008EDAB0 /* ArgumentParser */,
                            8B22BD29263E328B00867530 /* ComplexModule */,
                            8B22BD2B263E328B00867530 /* RealModule */,
                            8B22BD2D263E328B00867530 /* Numerics */,
                    );
                    productName = mandlebrot;
It may have been a little easier for me as I already had the ArgumentParser package on my second target that I just appended the 3 new lines to. However you could do the same and add a temporary package to your second target.
I then went in to Xcode and built the two targets like normal and it worked.