After updating to 3.0 or later, you might encounter an issue when loading saves from older version. It is clearly identifiable due to red skulls or other status effects being displayed over decoration or interactive items within the level, like so :

First of all, there is nothing wrong with your save. There are safe workarounds : 
- restart your run
- continue your save until you load a new biome, the issue should go away
- switch between custom and normal mode (unconfirmed - will essentially restart you run anyway)

This issue is due to a backward-compatibility loss during update 28 (on PC/console, bundle within 3.0 for mobile) which messes with items affects and status. It might have minor side effects within the loaded biome, if you encounter some weird artefacts or, less likely, crashes, please try one of the provided workarounds.

Enjoy !