Zotero is a popular reference management tool, and it has an add-on for PubPeer that lets you keep track of any issues raised about papers you cite.
This add-on can alert you to any retracted papers or concerns flagged on PubPeer, allowing you to avoid citing problematic sources.
Endnote helps researchers with citation management. It can automatically flag retracted citations, helping you avoid referencing papers that have been invalidated or retracted due to errors or ethical violations.
It also helps ensure your references are formatted correctly and consistently.