Hi and thanx for any help here, I trained nanite 1 had 5 rubies after doing so they dropped to 2. Why?!!!

Did you use the Merchant? Each use uses 1 ruby.

ok i do actually see the warning but i still think its in the wrong place... it should be their immediately after hitting merchant instead of after u select what each individual resource you wish to buy.

There is a pretty clear warning. Once you get to the transaction page, it states "Each transaction costs 1 Zorg Ruby!" Just like that. So... yeah, you lost your rubies on the merchant. A bit of advice: next time, trade with another player.