Clean but Confusing

I'm noticing a trend that places the search "submit" button/icon within the field itself. While I like the clean visual effect, I wonder if this confuses user. I know it confuses me when there's another, unrelated button next to the search field, per the examples below.

It took me a while to understand why the upload dialogue box displayed when I tried to search something on slideshare.com. NOTE: It seems that slideshare.com has increased the space between the search field and upload button since this screenshot was captured.

A colleague of mine kept hitting "new project" when trying to search for a project on InVision.

invisionapp.com