The only thing that comes to my mind is something about selecting the chain has changed in Cert-Manager. In Let's Encrypt production there is a default and alternate chain. Some ACME Clients allow choosing one or the other using the chain name.
A client could do this on staging too but the chain name is different. So you can get odd results using the production chain selection names when using staging.
Let's Encrypt recently announced plans for these chains to change in 2024. Perhaps Cert-Manager made some changes in anticipation? Or your config changed?