The minoxidil might have caused that to happen, but its not a bad thing.
I'm not sure how much you know about the hair growth cycle, but to put it in a nutshell each of your hairs grows (anagen), stops growing but remains in the follicle (telogen), gets shed, and regrows on a certain cycle that lasts a few years.
It is well known that minoxidil tends to accelerate the shedding of hairs that are in telogen stage. In other words, hairs that were close to or in the process of imminently shedding, tend to shed immediately after beginning minoxidil, and the three month time frame you mention fits perfectly with this condition. This is common, happens to a lot of people, happened to me, its mentioned on the Rogaine product literature, and in general most minoxidil veterans will tell you that it is a substance from which things generally get slightly worse before they get better.
The GOOD news is that these minoxidil sheds are caused by the chemical's effect on the follicle, and the follicle's response to minoxidil which is, in effect, clearing the follicle to make way for a new, minoxidil enhanced, hair shaft.
Anyone you talk to here on HairLossTalk.com who knows anything about minoxidil will tell you that its one of those things that you CANNOT judge until you have at least six months of usage under your belt (and at this stage you should start noticing some signs of "changes" in your hair quality), and a full year before trying to observe signs of regrowth.
You really have to be patient with ALL of these hairloss treatments. Due to the length of time it takes for hair to grow, cycle out, and cycle back in, they all take a long time before the beneficial effects start pumping out from the follicles in your scalp.
So.. hang tight!.. bite a bullet!.. and just try to relax and KNOW that you are using the strongest weapon that modern science has to offer to promote regrowth and thickening of hair. Hang in there!