Congratulations on your new Shopbot/Aspire purchase and welcome to the forum. If you create each cut as an individual tool path, the spindle/router will return home at the completion of each cut. To avoid that, you need to combine the cut files, which you can do IF these cut files are of course all made with the same cutter.... I think you do that when you save your cut-files.... (it is something I do without thinking, so I do it, but I don't really remember what I do..... )
But as to cutting things it shouldn't, I have no clue. I expect that any of the experts on board, will right off the bat ask you for more information before they can help.
To that end, to help shorten your cycle, can you provide information as to what machine you have, pictures of the problem cuts, screen shots of your right side "Toolpath" panel? Providing any of those things up-front will help you get help faster.
And can you populate your profile with things like your name, and what city you are in? It is more gratifying to help someone when it seems like you are helping an actual person. And it is easier to network with fellow Shopbotters if people know where you live. (As I live in Elgin, I was very excited to see someone posting from South Elgin. Because he was so close by, I made a point of getting to meet him which has been good for both of us. Had either of us not posted where we live, we wouldn't have made that connection. Of course, that is just my opinion, do as you see fit.)
Congratulations on getting cutting so soon after you bought your machine! It took me a year, from the time I got my Bot, until I even turned it on, as I had to remodel a room to put it in. Then I had to figure it out, which took a few more months........... Chuck
Chuck Keysor (circa 1956)
PRT Alpha 60" x 144" (circa 2004)
Columbo 5HP spindle
Aspire 9.0, Rhino 5