affirmative action: https://www.aclu.org/issues/racial-justice/affirmative-actio...
voter id (are all the other countries that have this violating their citizens' civil rights?): https://www.aclu.org/other/oppose-voter-id-legislation-fact-...
religious liberty (an employer engages in voluntary exchange... not much of a stretch to see it as a violation of rights to force them to pay for something which they consider blasphemous): https://action.aclu.org/secure/your-boss-has-no-business-you...
abortion (Roe v Wade federal overreach vs States' Rights... this and other issues like marijuana laws can be left to the States but "leftists" generally prefer a stronger central government over States as "laboratories of democracy"): https://www.aclu.org/issues/reproductive-freedom/abortion
ACA/"Obamacare": I couldn't find anything about their position on this issue but, if they were only defending civil rights rather than also being a "left-leaning political organization", I think they'd actively oppose forcing people to pay corporations for products they don't want.
There are plenty of good civil liberties related ways to look at race, but affirmative action is not one of them.
For example, I tried to find out if they took a position in Kelo v City of New London to defend property rights but my searches came up empty.
The supreme court agrees that affirmative action is constitutional (within certain bounds), see the recent Fisher v. UT case, or Bakke for the original example.
Almost all laws are constitutional, but very few pertain to civil liberties.
It isn't a matter of civil liberty.
A voter ID is not discriminatory in principle, provided that it's free (since otherwise it'd be a poll tax), and does not place undue burden on the citizen to obtain - like, say, traveling several hours to the only nearby place that issues them, and then waiting for several more hours in a line because it's understaffed to serve all the people that need to get their IDs from it.
The problem is that pretty much all voter ID laws promoted or passed in US to date fail these requirements, and thus effectively constitute voter suppression.
States' Rights limit the Federal Government from being so powerful that it can more easily violate civil rights... a bigger picture which ACLU should take into account.
Likewise, "legislating from the bench" may have protected some rights of individuals... but, far more often, it has "enshrined", as you say, new Federal powers at the cost of individual liberties.