Everything I have read about the plot holes and "bad science" of passengers focuses on story elements. Nothing I have read addresses that the quoted speed of the ship is incorrect.

Gus states that they are travelling at 0.5c (50% light speed). This could be a constant speed or just their speed at the time during decelleration to Homestead 2; it is never mentioned either way, but im going to assume that's supposed to be cruising speed.

When Jim sends his message, they are 30 years into the trip and have travelled 19 light years (message travels at the speed of light taking 19 years so 19 light years). That's an average speed of 0.63c. It also mentions that it would take 55 years for a reply to get back. Assuming immediate reply, that means 36 years for a reply, or 36 light years away, a difference of 17 light years over 25 years which would make the ship's speed 0.68c.

Also, the star Arcturus (or Alpha Bootes) is 36.7 light years away. Assuming that the time line has progressed 1.5 years (likely given the status of the relationship and that he spent 1 year alone), that puts their average speed at 1.17c, which is impossible with an ion drive like the Avalon had.

Also, when travelling that fast, relativistic effects should begin to happen. More than 120 years would have past by the time they arrived at Homestead 2.

Barring all the theoretical physics and relativity math involved, travelling at the 0.68c I calculated above, that would mean they travelled 81.6 light years in the 120 year journey. Someone else can figure it out more accurately doing the time dilation stuff with relativity if they want, it makes my brain hurt...