These are  in the 2.140 Opt-In.

1.  In the colony screen, the Sort by Research doesn't do anything.

2.  When meeting someone in mid-move, the "moves left" information in the info box in the lower-left of the galaxy screen doesn't get updated,  so it shows more moves than are actually left.

3.  The icons on the top row of the galaxy screen are strange at times.  One time I couldn't find how many Administrators I had left until I found the icon far to the right of where it usually is.  Another time the food icon showed I had 2, but I couldn't build a city.  The tool tip for food showed I had zero.  When I built a farm, the food icon still showed 2, the tool tip also showed two, and I could build a city.  When I built the city, the food icon showed I had none.

4.  Despite what I reported in a ticket I submitted about it, the notification about Administrators in the notification list on the left of the galaxy screen is still messed up.  It will show I need Administrators when I have plenty.

5.  When the BRAINY' AK event occurs, the notifications are messed up.  Why does the BRAINY' AK event occur?  It is useless now.

Playing multiplayer in the latest 2.1.4 opt in released on 5/16, and my friend playing the Yor doesn't get colonization events in order to receive ideology points. As the linked screenshot shows, he had colonized 4 non-precursor worlds, but since no colonization event occurred, he could not pick an ideology as indicated by it being greyed out.

http://imgur.com/a/BTPSy

Edit: After further testing, it seems I too won't get colonizing events on non-precursor worlds.

So did a bit of digging, we can add our own Starategic and Trade resources via the xml's. However we CAN NOT actually apply these resources to anything in game due to SD linking them into the StatTypes table (Scheme file which is not moddable), oversight, intentional or bug, either or all make this system completly unmoddable. 1 step forward and 5 steps backwards, sigh. Atleast prior to Crusade we could add trade goods

You cannot utilize the +25% logistics bonus from having a commander in a fleet.

When a command ship is in a fleet, the popup display shows that the logistics cap has gone up, but you cannot add more ships to the fleet. It appears that the increased capacity is factored into the display but not the actual fleet management calculation.

This is true on version <= 2.14 (opt-in) as of May 16, 2017

Mercenary "The Auspicious Start" is supposed to give 150 points to base influence of any colony while ship is stationed there. Did that and don't see any increase in influence though ...

I have also seen this in the current opt-in.

I have found that some the increased logistics can be used if the fleet and a single ship are moved together in the right way.  It doesn't always work.  I can get a 15% increase and sometimes a 20% increase if I do it the right way.  I never get the full 25%.  The right way seems to be moving the large fleet with the commander onto a tile containing a single ship.  If that works, try it again with another ship until it fails.  Trying to combine with 2-logistics ships first then with 1-logistics ships seems to get closer to the 25%.

In the fleet management screen there is no way to use the 25% bonus.

Beta-opt-in 2.14 of 5/16: "eyes of the universe" improvement appears to be bugged. Supposed to show only the AI homeworlds, but instead shows many other AI colonies as well.