This isn't a bug actually, but a logical 'code' built into the system. When your tech tree gets far enough down on one branch, the game then issues an 'equalizer' to stymie some of your reasearch by doubling the points needed.
If you spead around your research a lot, you suffer the most. It takes the lowest cost research you have, and doubles from that number, so if you're heavily reasearching government or military techs and have left a lot of blue or green techs alone, then you won't be as bad off as if you were branching out and trying to equalize your techs.
Your lowest cost tech might be 12 turns this way, but if reaching down just one or two branches, your lowest may still be 1 or 4, thus not impacting you. The AI suffers a lot with a few races who are coded to 'spread around' their research.
This should not have been added in ToA, but it was, for whatever reason some programer though it proper.