The Seagulls were sunk by first half strikes from Joe Pigott and Kwesi Appiah, before Oliver Norwood got a goal back from the penalty spot in the second period.
Shane Duffy and Jurgen Locadia both went off early but Hughton insists both were just as a precaution and said: "They were both very precautionary. What we tell all players with any little niggles or if they feel they've got to a level where they're not as comfortable with something, then come off and we'll deal with it.
"We'll see tomorrow. I'm hoping both of them are not bad but certainly they were both precautionary.
"We're hoping both will be available for midweek but we won't know until tomorrow."
On the match, Hughton said: "It was a good work out but probably we didn't turn up for the first half-an-hour and made life very difficult for ourselves.
"It shows the levels. They're a very well organised team and we expected a hard game and that we had.
"By the time we really got into the game, it was going to be difficult to get a result. We had very good chances and three really good opportunities but as regards a work out - we managed to play some of the young lads as well - it was exactly what we wanted.
"At this stage, we're looking to get 60 minutes into players. We have two games in midweek and will build it up to 75 minutes.
"It's never rocket science but you try to get to the levels you want come the start of the season. Sometimes you think you're not quite there and then you play the next game and it's all different."
Match report: AFC Wimbledon 2, Brighton 1Albion have made seven first-team signings so far this summer and asked about adding to the squad further, Hughton said: "At this moment we're happy with what we've got and we'll only bring in if we feel it's right for the team and for the squad.
"We're happy with where we are and we've got good numbers but we would tweak things if we can."
Reports in the past couple of days have suggested Albion have rejected bids for midfielder Norwood - who was on loan at Fulham last season - and winger Jiri Skalak.
Hughton said: "Jiri almost went out on loan last season and Ollie Norwood did.
"They are very much part of what we're doing here but there is an opportunity they might go. It's not something secret but what they have done is given us really good strength at this moment and both of them have worked very hard."