The way I got around this is by bypassing every instance of "setActiveSheet" or "activate."
For example:
var spreadsheet = SpreadsheetApp.getActive();
spreadsheet.getRange('A2').activate();
spreadsheet.setActiveSheet(spreadsheet.getSheetByName('Sheet2'), true);
spreadsheet.getRange('B4').activate();
spreadsheet.getRange('Sheet1!A2').copyTo(spreadsheet.getActiveRange(), SpreadsheetApp.CopyPasteType.PASTE_NORMAL, false);
can be shortened to:
var spreadsheet = SpreadsheetApp.getActive();
spreadsheet.getRange('Sheet1!A2').copyTo(spreadsheet.getRange('Sheet2!B4'), SpreadsheetApp.CopyPasteType.PASTE_NORMAL, false);
and can be run from any sheet on the document without changing the selected sheet or cell.
There may be a reason for Google to automatically add this redundancy, but this does appear to work in every case I've used it in.