Scan the area constantly
Obviously not every time you go into a stage, but the first could times you go to a new place or the same place at a new level, it’s good to ping the area all the time. You’d be amazed what kind of stuff is barely visible.
You find alternate paths a lot earlier than if you wait for a notification. You also can find and be ready for Pokemon that haven’t shown up yet on screen.
That’s actually how I found my first Metapod. If you check in this video, I approach the log going overhead and start scanning until I see a “???”, which means there’s a Pokemon approaching that you can’t see in any capacity yet.
Not only is this a great way to get a jump start on subpaths, but it’s really useful because sometimes the speed at which a Pokemon run through the stage can change at a moment’s notice so this will let you know where you should be aiming as you round the corner. This gets really useful in later stages where you can trigger events by throwing Illumina Orbs at specific flowers.