I'm not sure how that is happening if you don't have your note's text document open in a text editor while using the macro. If you don't have the actual note open in a text editor, the macro should always append to the bottom of the note's text document. If you've got the note's text document open and are actively editing it, and you're leaving the cursor at different points in the document, all while sometimes invoking the quick note macro and using it to also append to the document, then I can see how you might encounter problems.
The quick note macro is designed so that you can create or append to a note without opening the note's text document itself in a text editor (e.g., TextEdit). I made it that way because I didn't want to have to open or switch into the text editing app while taking notes (i.e., to manually insert the note directly into the note's text document via TextEdit). Operated in that way, with the actual note unopened, the macro automatically appends to the end of the note's text document, and I never have to leave the main app I am working with, or if I'm just noting down thoughts during a conversation, I don't have to open the text editing app or switch to it in order to take a note.
So, if you've got the actual note's text document open (e.g., in TextEdit) while you are taking notes via my macro, you are not using the macro consistent with its design and proper functioning, and it may insert text in a place you don't want it to, or it might not register the text entry at all. Further, if you're just going to have the text editor open while you take notes, you might as well enter the notes directly into the text editor where you want them rather than use the macro.
Bottom line: adding some elements to the macro to switch you into the text editor document and then scroll to the bottom of the document is surplusage which defeats the purpose of the macro and makes it something that is cumbersome and unpredictable rather than quick, reliable, and truly convenient. But if that's what you want to do, it's easy to insert an "Activate specific app" action followed by a keystroke like command-arrow down to get to the bottom of the document.