Edit: We suspect that some ruins are not explored because of map trading and events that reveal system maps. Since those systems are then flagged as "explored", explorers never go there and thus never explore the ruins contained in those systems. If explorers were set to re-explore again and again once they have done the entire galaxy, they would eventually come back and find anything that was missed.
As it stands, I suspect every planet has a single boolean value for your race's "explored" status. If it's set, you can see it's resources. The status of ruins is set separately. As such, if you get sector maps as a result of map trading/theft/discovery, all the planets with ruins are marked as "explored" and your explorers never go to them to check out the ruins. So, you're left with a situation of idle explorers late in the game, when there are still ruins to check out. Exploration needs to check TWO flags - both "explored" and "investigated". Not ONE as it stands.
Additionally, the "explored" flag is still not set correctly when an explorer visits a planet. Occasionally, planets resources are revealed but the ruins are ignored. This could be a logic issue - such as the "explore" function called when it's a certain distance from the planet but "investigate ruins" done from a closer range - which the explorer may not achieve in that one pass (eg: chased off by a monster or hostile ship). Or possibly the explorer needs to be close to the planet for a period of time - again missed occasionally because of being chased off, or perhaps faulty logic (decision to move off to next target made before investigation time has elapsed).
Regardless of how it's happening, it's never been fixed.
“That which can be asserted without evidence, can be dismissed without evidence.” ― Christopher Hitchens