Not a bug, from the changelog:

• Ideology cost goes up equally in all categories to encourage players to pick an ideology and stick to it.

No, its cost increases if you unlock a trait from a different group.

I use the Pragmatic choice for 50 turns of peace.  I lost it when I chose another Pragmatic perk and spent my Pragmatic Ideology points.  It happened by my own clumsy misclick, and I was upset with myself.  I had to switch to military development when I had not planned to.

This is the confusion. You are not awarded anything. You have sufficient pointage to unlock an ideological choice at its current price, hence it is lighted up. If you choose instead to buy something else with your ideological currency, then the price increases on everything else you didn't buy. So you need more points to pay for it and it is no longer lit up.

No Bug here, Courtneyme109 is just simply not happy with the change that points increase in EVERY tree as  you take Traits, you know like the Dev said to him in his post. Yet continues to argue the fact.

yep and it has been like this for a long time(way before crusade)

the only change is that now the price goes up by 10 for every ideology,

instead of going up by 10 for the ideology you choose and 5 for the other two

The Ideology Tree is for me, the single most unrealistic and immersion-breaking feature of GalCiv3.

The central issue is less that you can get the 3 constructors from Pragmatic and then get the warship from Malevolent (ie merrily go back and forth between the 3 trees) but that you can do that at no real disadvantage. Races that aren't your ideology will hate you anyhow. The UP don't get that upset about if, if they ever meet.

Ideology should be something you choose and then the game forces you to stick to. Break your idealogical leaning enough and bang goes the next election and your colonies are suddenly easier to culture flip, the UP pass resolutions against you, place embargoes on you and heck, even the Drengin think you're disgusting, evil and untrustworthy...

Ideology is an interesting problem. Arguably your actions should dictate what Ideology you are unlocking (somewhat, as it does now), but it gets quite odd, quite quickly, and your ability to cherry pick is too strong in my opinion. If I could, I would have modded the system as such:

Ability Chain A )

Choice 1/2/3 (Corresponding to ideology)

Ability Chain B )

Choice 1/2/3

Etc.

When you have X many ideology points in Benevolent, you can choose to unlock Choice 1 in either Chain A or B. Doing so though, is mutually exclusive with Choices 2 and 3 of that chain. 

So for example:

Ability A) Colonial Policies

Choice 1) Freedom to Explore! Colonists are happier (being purely volunteers), but grow slower.

Choice 2) Incentive based Colonialism! Colonies grow faster, but have a small fiscal penalty when not pop-capped.

Choice 3) Forced Migrations! Colonies grow much faster, but happiness takes a big hit until pop-capped.

I'm sure you can guess how these are laid out. The point is, you can be "Malevolent" regarding your Colonial Policies, but perhaps you choose "Benevolent in another category. You cannot be Malevolent AND Benevolent in your Colonial Policies. You have to make a choice and sacrifice some opportunity. This also has the bonus of allowing the B,P,M mixture of ideologies to produce combinations that might actually seem realistic.

Communism might be a "Malevolent" force in population matters, but fairly Benevolent in economic matters, and down the middle in terms of military aggression... the Soviet Union having forced many populations to relocate, but in theory having the people's interests at heart, and again, in theory, being a "peace-loving" nation. 

The Capitalists of the era wouldn't have been much different, perhaps a bit benevolent in some areas, pragmatic in others, and such.

With this system the "Ideology" of the player is rarely ALL B-P-M, (you'd have to be purposely choosing one line only) its the unique combinations of their actual policies. Those combinations are INFORMED but not entirely DICTATED by your choices in colonial events and such.

Yup that's fair too. An effective discount for being "purer" to your leading ideological element.