Sometimes, web applications overflow the region the window manager assigns to them. See for example the following picture:

There are two issues there:

• The webapp is wider than the screen area, which can be noticed by the background image that is not centered.
• The webapp is also longer, and it occludes the bottom area where the homescreen bottom bar should be present.

Facts we have gathered:

• It can happen to any web application that paints to the layer used for standard applications, not only to the launcher (in the picture).
• It's apparently random, around 1 out of 5 restarts presented the result in the picture, on a Minnowboard. No clear reproducer found so far.
• It isn't related with a specific hardware, it's been reproduced on Minnowboard and Raspberry Pi 3.