There are a whole slew of reasons. At least a dozen. Some I can recall just now are.

This was a minor issue in the past as there weren’t many people doing it. Like all such things, it can become a problem when many people do it.

Many Boat owners in a marina - most of them, in some marinas - don’t like liveaboards and complain to the management. They feel that a marina should be for yacht owners not sea nomads. If they are paying for a certain kind of ambience, then they have a right to complain.

Liveaboards often hang laundry on the deck of their boats. This winds up the yacht owners. They feel it makes the place look like a trailer park.
The boats can get scruffy, and often accumulate loads of deck junk.
Sometimes they even use the pontoon as external storage.
Liveaboards will usually put an extra load on the marina facilities and services. They are going to use the showers, toilets, laundry and anything else much more than the yachties. This can use much more power than is normally the case and this extra cost has to be borne by the marina.

Some local authorities may have a prohibition on residential berths. This would be due to zoning restrictions: no residential use. Therefore the marina management will be getting grief from the city authority.

If residential use is allowed then there might be a limit on the number allowed. This means the marina have to police it or get problems with the city.

When some residential use is allowed, the city officials often visit and take berth details, boat names, owner’s names, check taxes, check any other licence requirements. The marina have to stay up to date with who is a liveaboard or not as the city are always breathing down their neck. It is a mega pain for them and if some extra liveaboards are reported by yachties the marina gets more pressure from the city.

City inspectors want to find the registered liveaboards at the same berth all of the time. They probably think of it as a street address or something. I think this is more likely related to an unwillingness to walk the dock looking for the boat. So if liveaboards change berths, it’s yet another thing the city kicks the butt of the marina about.

Some liveaboards may not be boaters, and this can cause issues: when hard weather blows in, these boats might have crud blown off the deck, or come adrift, or experience or cause other problems related to knowing nothing about boats.