Wow... There are so many red flags in your post that I lost count. You two need to reconnect with each other before you even think about swinging again. Swinging is a way to enhance your sex life, not replace it. I think you already know this though since you've already been swinging for a few years.
Quit swinging immediately. Don't let this slide. There is obviously something wrong with her feelings and I don't feel she's being honest with you about them. Did she ever let "that time of the month" interfere before with sex? If something seems or feels wacky, it usually is.
... If this event felt wrong, it's because it was. Does she usually carry condoms in her purse for that "just in case" time? Do you usually spontaneously meet males for threesomes on a whim or do you usually plan these events? Does she usually buy the condoms? If not, then something other than, "I was trying to be safe in case..." was happening here. The job of condom buying is up to my husband, and really, we only buy for ourselves. We don't buy condoms that don't fit. Others usually bring their own.
Don't you set things up together? I mean some couples don't, but we do. We discuss everything together before plans are made. I'm seeing a total lack of respect on her part regarding you. If what she says is true, there's no respect for what YOU want to have happen. She is very concerned about what she wants, however. Does sex really mean this much to her? She's willing to risk her marriage for sex? I'd be questioning the trust I'd be having as well. You might want to trust her, but does she really think you're that naive?
Sounds like maybe marriage counseling is in order too, because NOW, she's cheated on you. You both need to sit at the kitchen table and talk NOW because you DO have a problem! Putting this off is not helping your marriage. Maybe in hopes of putting it off she's hoping this will all go away. Also, maybe in her mind, she didn't do anything wrong, but really, deep down, you know this isn't swinging. She's crossed a line and you two need to find a way to get it back on track. You have no idea how much I wish for the two of you to get your marriage back on track. You need to find out why she's doing what she's doing. Deception has no place in swinging or in a marriage.
Good luck to you both and a belated Welcome to the Board. You'll find quite a few people here who give great advice as there are years and years of swinging experience here.