When the app file is downloaded from the Internet and launched on the iOS simulator, the error dialog boxes “"..." can't be opened because Apple cannot check it for malicious software.” and “"..." is damaged and can't be opened. You should move it to the Trash” are displayed on the Mac rather than the simulator. This is due to the fact that the app file is not properly signed.
If you know that the app file is trusted by your company, after opening the Mac Terminal and running the following command, install the app file into the simulator to avoid having error messages displayed for that app file.
xattr -dr com.apple.quarantine <.app file path>
Although one option is to sign the app file, as the app files are not usually distributed outside the company, there is little advantage in trying that hard.