Had an annoying stuff-up the other day. I'd booked a flight from SYD-LAX on UA, using my UA FF# at the time of booking to get E+ on domestic legs. When I got to check-in I gave them my BD FF card but the check-in agent apparently didn't apply it.

I noticed after I'd boarded that the boarding pass only had my UA FF# number on it, so when I landed at LAX I tried to find a CS agent. The best I got was a check-in agent who confirmed that UA had credited my miles to MP. She also messed up my PNR so I now no longer have E+ for my domestic legs, but do have my BD number applied for the remaining flights.

I know how to fix the E+ issue, however I'm wondering if I can fix the fact that I now have 7500 miles on a UA account that I'd much,much rather have on my BD account. The UA agent said I should call BD first, but since UA have the miles should I be calling them? Is this even possible to fix?

From past experience, no. I have a dormant SK account so when I make a reservation on SAS website it automatically picks up my Eurobonus number. On a recent CPH-SEA flight which I booked on SK website, I changed the FF number to BD at check-in. Even though the BP had BD*G, miles were posted to SK. Could not get the miles transferred to BD as BD said miles once posted to another program can not be posted/trasnferred to BD.

Technically, it can be done. The miles need to be unposted and then reposted to the appropriate program, but that is a lot of hassle and the FFP terms usually exclude the possibility of changing the destination of the miles once the segment is flown.
In case of agent error, you might have a case (you would have to follow it up with UA rather than BD) but documenting it when your BP said UA and you did not pick it up before flight might be difficult. There is also the added difficulty that, IIRC, the terms of the EPA programme (I assume that this is on this basis that you get access if those 7.5K miles are orphaned) specifically require the use of your UA MP#, to the exclusion of other FFPs. IMO, you are on a difficult battle here.

I've had similar issues earlier this week.

It seems that some UA and US agents simply don't know how to put in the BD # correctly.

I'm missing totally 8 segments. At least they didn't post to UA/US -- that would make it more difficult to un-do.

Funny that....I had the same problem on UA SYD-LAX last year and was eventually able to erase the miles in UA account and credit to LH. The same thing happened to me again this year and I have yet to call UA to ask them to delete the miles and then call LH to ask them to credit again. It's a real hassle but it works if you get the right person on the phone....

Even if you have your BD*G FF number posted on your UA boarding pass it doesn't mean that the flight will actually post to BD. Couple of my flights posted to United instead and this was after I had made sure that both of the FF numbers were correctly put to the itinerary. One for the status benefits purposes and one for posting.

The only way to ensure that the miles will go BD is to ask the agent to entirely erase your UA MP number form the itinerary. It shouldn't be like this but this is UA after all.