These aren't considered 90° elbows - they are signal egress points. Although there are times when you need to control the angles of top traces with respect to bottom traces, each layer should be treated as a single entity. The only 90° traces you see should be at TEEs.Finally this Semtech example uses 90° in several places, particularly when using vias. That is apparently not because a 45° can't be used for those transitions. There are additional examples in the discussion.
Source: AN1200.04 RF Design Guidelines (no mention of bend angle)
As for the original post, what you see is what happens when you move the part (for whatever reason) after you have performed a DRC and don't adjust the traces and don't do another DRC.
Turn on the 45° setting in your routing package and leave it on.
