A pop at the end of the shot, sometimes with a splash of water from the top of the cylinder, is caused by a compressed air pocket above the water column releasing pressure. The pop will not harm the machine, but we can eliminate it.
Why it happens
When the piston retracts at the start of a shot, the water column drops onto the top of your coffee puck and immediately fills the headspace. Ideally the top of the water column meets the bottom of the piston. However, under-dosing the basket, a step-down basket that seats the coffee lower, or not filling the water cylinder fully, will create an air pocket between the top of the water column and the bottom of the piston. That air is compressed during the shot, and when pressure releases at the end, it creates a pop sound. If any water is sitting on top of the piston, some may splash out.
Common causes of excess headspace
Under-dosing your basket: e.g. 16g in a basket with a nominal 18g dose.
A step-down basket: it seats the coffee lower and creates extra headspace by design.
Not filling the water to the top of the cylinder before each shot
Grinding too fine can amplify it too as finer coffee takes up less space in the basket.
How to make it disappear
Dose the basket properly and fill the water fully: for most people this alone eliminates it.
Add hot water from a kettle while the piston is retracting at the start of the shot. It flows down and fills any remaining headspace.
Adjust the Brew Volume (Context Button → Brew Settings → Brew Volume) from 100 mL to 80 mL to reduce the headspace (coming in a software update).