This may be way off base, but we also have a number of old systems still kicking around from the .NET 4.X era and have inherited solutions that "have history" ...

Most of the time we have run into this kind of problem, it was cause by a non-standard page declaration. (someone changed the code file to point elsewhere at some point in time, but didn't clean up the old files)

<%@ Page Language="C#" AutoEventWireup="true" CodeFile="CourseReport.aspx.cs" Inherits="CourseReport" %>

Was change to something like:

<%@ Page Language="C#" AutoEventWireup="true" CodeFile="/code/CourseReport2001.aspx.cs" Inherits="CourseReport" %>

and we find ourselves making changes to the file CourseReport.aspx.cs ... still located in the same directory as the ASPX file, expecting to to work like all the other pages in the solution.