Why can't KHL or MHL players be signed?
 

Can someone explain to me why you can never sign players from the KHL or MHL that you have the rights to? I always get a message that says players can't be signed from those leagues. How do you sign them after drafting?

You have to wait until their KHL contracts expire; unlike most of the other European leagues, there's no transfer agreement between the KHL and NHL, just a memorandum of understanding to honour each other's contracts. So an NHL team can't simply sign whichever KHL player it wants. There may be some backdoor ways around that, like having the player buy out his own KHL contract, but that presents some problems for the game - for one, the NHL team would have to give the buyout-earmarked money to the player in the forum of a bonus. We don't model guaranteed bonus money separately from regular salary in the game right now, but if we added that option for buyouts, we'd need to start doing that so the proper restrictions on bonuses could be enforced. That's particularly relevant for younger players; the Leafs got into trouble with the league that way a few years ago because they paid Jonas Frogren a bonus that was too large for an ELC, which he used to buy out his contract in Sweden.

MHL players should be signable directly, assuming they've been drafted and aren't already contracted to a KHL team.

But when?
 

This has been a serious issue that has cost me several players drafted in the first round over the seasons. When is the window to sign players who become free agents from the KHL? It seems like their contracts get renewed automatically with no free agency window. I've watched players I drafted have their KHL contract tick down to one year remaining, and then I never see a time when they are eligible to be offered a contract, next thing I know they have a brand new 3 year KHL deal.

Because they have to be registered as Free Agents on July 1st. It's the risk you take with drafting players who are in the KHL.