Let's tell the story from the beginning. I have several long expressions that I want to make more compact on the screen by replacing the variables r1 and r2 with
HoldForm[expression] /. {r1 -> Subscript[r, 1], r2 -> Subscript[r , 2]}
I then copied the result to the initial expression. At this point, I realized that the syntax highlighting did not change in the [r, [Theta]] functions: the variable r is colored green whether it is with a subscript or not. After some research, I see that the Symbolize function should be able to solve this problem. Finally, to check that my expressions are still correct, I use a formula with partial derivatives and this is where I discover an inconsistency due to a hidden HoldForm.
I don't know if this can be considered a bug, but I think Wolfram could improve Mathematica by:
1) ensure that there are no hidden commands that can be copied without the user's knowledge
2) if the variable Subscript[var, i] is defined as a symbol with Symbolyze, the syntax highlighting of var in Subscript[var, i] should no longer be active when this subscripted variable is used in a function