My test project .aiproj file has 4 duplicate entries like this:
<PropertyGroup Condition=" '$(Configuration)' == 'DefaultBuild' " />
<PropertyGroup Condition=" '$(Configuration)' == 'DefaultBuild' " />
<PropertyGroup Condition=" '$(Configuration)' == 'DefaultBuild' " />
<PropertyGroup Condition=" '$(Configuration)' == 'DefaultBuild' " />
I remove the duplicates, check it in, and when I open again it adds a new duplicate.