G’day all,
for info I had this exact issue with my 2016 Skoda Octavia RS wagon. Thanks to the advice on here I replaced the boot lid latch (new part number is 8R0827505a) and this has fixed the issue. The part number for the sedan/hatch is different (it starts with a 5). The fix itself is very easy, just use a door trim remover the remove the trim (lower section on tailgate interior). Remove the plastic cover over the latch and then disconnect the 4 pin plug to the latch, unbolt the latch (three nuts) and remove the latch. There’s a small plastic clip holding it in place which can be squeezed together with small pliers and then easily pulled out. Then just reverse the process to replace.