This can happen in a few ways:
1. whatever exports the metrics, does so with a timestamp, but actually changes the value on you between scrapes without updating the timestamp. This is relatively unlikely unless this is something very specialized.
1.1 or it actually exposes the same metric twice within one /metrics response – but the official client libraries actively prevent that
2. (more likely) after all relabeling, you end up with metrics from multiple targets without any distinguishing labels between them.
Are you scraping through some kind of proxy? In general, Prometheus expects to discover and access each target individually, so that it can separately collect the data from all of them.
Look at the raw metrics endpoints that Prometheus would scrape – if they do not have duplicates or timestamps, it must be 2. Remove label drop or replacement rules that may accidentally coalesce multiple targets into having the same labels, especially if you are messing with the "instance" label. Looking at Prometheus' target page may also help in identifying targets that have the exact same label set.
/MR