I had a similar situation happen on another car. It turns out that the brake system and clutch system share hydraulics through the brake fluid reservoir and that the reservoir was low. I added fluid and haven't had a problem since.

96 Contour SE Duratec V6 24-valve 2.5L ATX 108,000 mi. Replaced: crankshaft w/ DMD, EGR valve (clogged), EVR, DPFE, PCV valve, evap emissions hose & tube (cracked), window regulator (broken), LH & RH PCV tubes, UIM gasket (leak), ignition coil