Rashi quotes the medrash that when Ya'akov saw Ephraim and Menashe he initially refused to give them a beracha because he didn't know who their mother was. It was only after Yosef showed Ya'akov his shtar kedushin and kesuva that Ya'akov agreed to bless them.
Two questions come to mind. First of all, what was bothering Ya'akov? Was he really concerned with who Yosef married? Shimon married someone fron Cana'an according to one pshat and Yehuda eventually married Tamar who did not have a great lineage. Furthermore, if Osnas was Dina's daughter didn't Ya'akov know that? Secondly, what did Yosef hope to accomplish by showing the shatr kiddushin and kesuva and how did this appease Ya'akov.
I believe the key to the answer is to understand what Ya'akov was trying to accomplish. The berachos that Ya'akov was giving Ephraim and Menashe were not just stam berachos, the intent of the berachos were to make them into Shevatim. In order to be considered Shevatim Ya'akov had to insure that they had the appropriate lineage. However, he wasn't concerned where Osnas came from, but rather he was concerned over what type of relationship Yosef had with Osnas-was it a real marriage or was she his pilegesh.
I heard recently a shiur from Rav Belsky that I found online, where he explains that when Ya'akov moved into Bilhah's tent his intention was to change his relationship with Bilhaha and Zilpah from being his pilagshim into being his wives. In other words he was koveia that they were no longer shifachos but had the status of imahos. The purpose of this was to ensure that all 12 sons would be fit to be shevatim. If Bilhah and Zilpah would retain their status of shifachos then their children would only be considered avadim and not part of the shevatim.
Reuvain did not understand this and he thought Bilhah was still his father's pilegesh-that's why the posuk says he slept with the pilegesh of his father. The Torah is describing the mindset of Reuvain. Rav Belsky further pointed out that after this ma'aseh, the Torah constantly refers to the shevatin as "12 sons of Ya'akov" and as "achim/brothers". The Torah is stressing this point that all 12 sons were shevatim and even the children of Bilhah and Zilpah were no longer considered avadim but shevatim.
With this idea, we can understand the whole conversation between Ya'akov and Yosef. In order for Ephraim and Menashe to be Shevatim, they couldn't be sons of a pilegesh. They had to be children of a real marriage. It's possible that even though Ya'akov was able to change the status of Bilhah and Zilpah (and consequently the status of their children) retroactively, when it came to Yosef's children he couldn't do that since they were already starting at a lower level having come from Yosef and not from Ya'akov. (You can also probably take issue with Rav Belsky's hanacha that originally Bilhah and Zilpah were only shifachos, maybe they were always imahos just Reuvain did not realize this).
The Ra'avad in Hilchos Ishus 1:4 writes that a pilegesh has kiddushin with no kesuva. The Maggid Mishna says this is also the Rambam's shittah, however the Lechem Mishna writes that from the Rambam in Hil' Melachim it seems the Rambam holds a pilegesh has no kiddushin and no kesuva. Either way, (although it works better with the Lechem Mishna), we can unde3rstand why Yosef responded by showing Ya'akov his shtar kedushin and kesuva. He wa sshowing Ya'akov that Osnas was his real wife andnot just a pilegesh and therefore his sons were fit to be made into shevatim.
(Ayin Sha'arei Aharon who mentions this idea as well)