The issue is called in official channels "Operational Sovereignty". Without source code for the aircraft you have no operational sovereignty over its use, meaning America can unilaterally prevent you using the aircraft if it wanted to. I'm wouldn't know if it can be done instantaneously or not, but it certainly can be done. Ask the Iranians what happened after the Shah was deposed when they tried to use the Tomcat weapons system? I think they lost at least Two aircraft that way.
Making the statement that American/British/Australian interests will always synchronise during the life cycle of the aircraft is highly dangerous.
By not investing in, and having access to, the source code effectively now means that whatever future the British Military aviation industry thought it had is now gone. It is condemned forever to build components only, because the real knowledge is encapsulated in the software, and you cannot catch up, especially after the USA keeps investing in the software for the next Twenty years. Furthemore, if you think you are going to integrate home grown ordnance, think again. You just lost that industry as well.
Arguments about patents and intellectual property are specious. All countries reserve the right to ignore patents for defence purposes.
As for software bugs, yes they do exist. apart from the well known incident when F22 Fighters crossed the International dateline, guess what happened the first time an (Australian) F18 attempted to fire a Sidewinder missile in the Southern Hemisphere?
One solution to this mess would be to put the software in escrow - meaning that you could have access to it in extremis.