If United States patents can be discarded at will by global markets, it creates serious intellectual property concerns for research and development groups in the US.

Without a possible profit incentive, what will incentivize drug companies to spend billions on cancer medication or other research if the compound will be lifted from them the next day and sold at pill cost, not compounded R&D cost?

It's definitely in US interests (both public and private sector) to strengthen the value of a US patent and US patent law globally.

Why would a government not argue in favor of this?

Pretty simple to deduce. Bayer is probably a pretty big donor to various politicians. I wouldn't be surprised if high-level US officials have tried to pressure Indian officials with other things to make sure this works for American companies.

They've done it time and again with copyright law.

So much of what America produces is intellectual property. If India wants to take it without paying, when then America should stop buying Indian products.

The problem is both sides are being assholes here. Bayer is charging WAY to much for the Indian market, but the compulsory license is way too cheap.