Steps to reproduce:

1. Run flutter pub get in a module with plugins, like the samples flutter_module_using_plugin. See README for details.
2. Run pod install in the host app like samples ios_using_plugin.
3. Open the host app xcworkspace and build for the simulator

ld: warning: ignoring file flutter_module/.ios/Flutter/engine/Flutter.xcframework/ios-armv7_arm64/Flutter.framework/Flutter, missing required architecture x86_64 in file flutter_module/.ios/Flutter/engine/Flutter.xcframework/ios-armv7_arm64/Flutter.framework/Flutter (2 slices)
Undefined symbols for architecture x86_64:
  "_OBJC_CLASS_$_FlutterMethodChannel", referenced from:
      objc-class-ref in EspressoPlugin.o
  "_FlutterMethodNotImplemented", referenced from:
      -[EspressoPlugin handleMethodCall:result:] in EspressoPlugin.o
ld: symbol(s) not found for architecture x86_64
clang: error: linker command failed with exit code 1 (use -v to see invocation)

flutter pub get copies a release version of the Flutter.xcframework to a known spot in the module (.ios/engine).
When the host app builds, it runs a Flutter script (xcode_backend) that copies the correct build mode version of the framework to that spot, depending on the mode you're building the host app in (Debug in the case of running the simulator). However, if you have plugins in the host app they build before the script runs, you get the linker warning because it's trying to link on the release version of the framework, and the app won't build.

Probably made worse by #73072 which changed the copied framework from debug (which can fail on archiving) to release (which can fail on the simulator).