I am not sure if this is a problem with the most recent Beta or was already an issue before 3/5 but I am seeing a difference between earlier versions and this one in the handling of links.
I have been using the Notes feature quite a bit. I copy text into the Note and then go back to the source. There I click on the place where I am citing or scroll so this place is the top line in that window. Then I hit: CTRL + ALT + C. I then select a phrase or word of text in my note, click in the url window in the menu bar of Notes and hit CTRL + V and then ENTER.
By this, I have been able to "bookmark" where I get each quote much in the same way that Clippings works, but with the flexibility of a Note file. It's more work than just using Clippings but I have recently been using this approach alot more.
The place marked in the source text has been fairly precise in previous versions (usually within a few lines or so), but not now.