You need to catch Dust Shades to collect Bottled Ectoplasm but there are a few different means of doing this. You can just run and jump after them, but that's unlikely to be very useful. Instead, you should make use of your abilities such as Dash and Zipline to move more quickly around the boat. You could also catch them with Lightburst, as you'll collect the Bottled Ectoplasm if the Everlight touches the Dust Shades.