Right now your upper body part has no connections. This can cause the game to glitch. Also, the game tends to glitch, causing creatures to suffocate, if it tries to add a part
before the part to which it is connected. It will still work fine in-game except that they always keel over and suffocate. I have had that happen to me several times. Your problem is that your head is connected to your neck, but the neck body part has not been added yet. This would cause this glitch to appear. Also, the [HEAD] tag is not required, that isn't the problem, but you should add it because if not your eyes, mouth, ears, and nose will not be attached. One last thing that I decided not to fix below is that at the moment all of your organs are attached to the [UPPERBODY] tag, not the UB body token. This means that your upper spine, your heart, and the other organs are all connected to the energy connector. You could fix that problem by creating a second set, and replacing all of the tag [CONTYPE:UPPERBODY] with [CON:UB]
As this is all pretty confusing, I also added a changed version below.
Body
[BODY:NEWCREATUREMAIN]
[BP:REALUB:primary energy connection][UPPERBODY][SKELETON]
[BP:UB:upper body][CON:REALUB]
[BP:LB:lower body][CON:REALUB][LOWERBODY]
[BP:NECK:torso-head connector][CON:UB][SKELETON][THROAT][BREATHE]
[BP:HD:head][CON:NECK][MOUTH]
[BP:RA1:right arm connector][CON:UB][SKELETON][RIGHT]
[BP:LA1:left arm connector][CON:UB][SKELETON][LEFT]
[BP:RA2:right arm][CON:RA1][LIMB][RIGHT]
[BP:LA2:left arm][CON:LA1][LIMB][LEFT]
[BP:RH:right hand][CON:RA2][GRASP][RIGHT]
[BP:LH:left hand][CON:LA2][GRASP][LEFT]
[BP:RL1:right leg connector][CON:LB][SKELETON][RIGHT]
[BP:LL1:left leg connector][CON:LB][SKELETON][LEFT]
[BP:RL2:right leg][CON:RL1][LIMB][RIGHT]
[BP:LL2:right leg][CON:LL1][LIMB][LEFT]
[BP:RF:right foot][CON:RL2][STANCE][RIGHT]
[BP:LF:left foot][CON:LL2][STANCE][LEFT]
Creature
[CREATURE:NEWCREAT]
[NAME:energy thing:energy things:energy thing]
[TILE:'U'][COLOR:3:0:0]
[GENPOWER:3]
[INTELLIGENT]
[CANOPENDOORS]
[BENIGN]
[PREFSTRING:stature]
[BODY:NEWCREATUREMAIN:2EYES:2EARS:NOSE:2LUNGS:HEART:GUTS:ORGANS:THROAT:SPINE:BRAIN:5FINGERS:5TOES:MOUTH]
[SIZE:15]
[MAXAGE:100:210]
[ATTACK:SECOND:BYTYPE:GRASP:punch:punches:6:12:BLUDGEON][ATTACKFLAG_WITH]
[ATTACK:MAIN:BYTYPE:MOUTH:bite:bites:5:10:GORE][ATTACKFLAG_CANLATCH]
[CHILD:18][BABY:1]
[FAT:3]
[EQUIPS]
[DIURNAL]
[TRANCES]
[NOBLEED]
[SEVERONBREAKS]
[SPEECH_MALE:human_male.txt]
[STANDARD_FLESH]
[HOMEOTHERM:10067]
[LAYERING:10]
[SWIMS_LEARNED][SWIM_SPEED:2500]
[MUNDANE]
[CURIOUSBEAST_ITEM]