Here are all the issues I experienced in my first completed game. Some of these may have been fixed since I started the game in 1.02 and finished in 1.1 but, they all were still present in my game at the end.
The resource box in the upper right hand corner doesn't have a place for the thousands place. (Confirmed still present with 1.1 new game)
Text runs out of boxes if extracting more than one resource. (sometimes however, can't find an example at the moment.)
Star Bases prompt for an upgrade if they have 1 module available and there is a dual module available to build (just doesn't allow one to build they have to pass). (Confirmed still present with 1.1 new game)

In the diplomacy screen there is a green line to each allied race which isn't needed as allied races are already in the green shaded circle. (Confirmed still present with 1.1 new game)

A space in the planet screen when the icons indicating the manufaturing points switches between large icons to medium.

The Terrian Alliance won the UP resolution for the UP headquarters, however, is 14th on the power list and shouldn't have been able to be voted on as it's not one of the top 6, sorry no saved game for this.... (Confirmed still present with 1.1 new game)
example of Trinary are not showing as a member voting and they are #2 (must have left the UP)
Yor Singularity is showing voting though bottom left and they are #6, they are a member of the UP as they still cast a vote yet is not an option to vote for.
Qaulite Searchers are #7 in the power ranking and are also members of the UP as they are in the middle row just offset to the right voting.
So if they are voting for the top 6 the options should be Zapoids (me) A, Noveny Colleccio B, The Wirling Spawning C, Galactic Simulations 3.0 D, Yor Singularity E, Qualite Searchers F. Even if there was some flux in power between the vote and the diplomacy screen (both same turn) The Terran Alliance is #12 and the Loomite Parasitic is #28, which I don't believe is possible.

Precursor Hull Reinforcement ship part has no mass and can be built as many times as possible on a ship making it have an unlimited amount of hit points. I confirmed this is still an issue using the Thalan tech tree and using the cheat unlock. Also this is not using any mods as Paul suggested and the original game was just using tech trading/researching. I sped things up in the test in 1.1 to see if still present using unlock and it is...the picture below shows many many Precursor Hull Reinforcements which don't require a resource or have any mass and have many on this ship with 0 points used. (Confirmed still present with 1.1 new game)

Multiple crashes yet when destroying specific buildings.... doesn't happen every time on same buildings unfortunately I deleted the debug file/save game 
I declared war on 10-15 races and then the very next turn they all asked for peace, why can the computer players ask for peace right away where the human player has to wate?
Turn time was still high 3+ minutes. (Confirmed still present with 1.1 new game)
Jumpy Ship Movement is still present updated my ticket... (Confirmed still present with 1.1 new game)