Have had MapFactor installed on both Android 2.3 and 4.4 on different devices, and both had an issue with wrongly exiting me at random motorway junctions and then immediately rejoining the same motorway. Have had the same error occurring on both NewZealand and UK maps.
IMHO it is connected with map, speedrestriction tags. Look at the osm map and add it to this road. 1. https://www.openstreetmap.org/ 2. Login 3. Edit (I reccomend in POTLATCH). 4. Klick on the road. 5. Klick on restriction sign. 6. SAVE!
Try also set road preferences - higher for motorway (eg 56 or 63 or 69). It works!