Physics=A on a helper can result in clones. Physics=A automatically changes players to the landing state (52) when reaching the ground, and you don't want that on a helper.
For the going through the floor part, most likely it's the opposite, having no physics on Marisa when she should be having A.
Okay, removed physics=A from the helper. About Marisa herself:
;Jump Medium Attack
[Statedef 610]
type = A
movetype= A
physics = A;N
ctrl = 0
anim = 610
;velset = 0,0
sprpriority = 2
[State 610, STS]
type = statetypeset
trigger1 = animelem = 2
physics = N
[State 210, VOICE]
type = playsnd
trigger1 = animelem = 4
value = 210,0
channel = 0
[State 210, 1]
type = PlaySnd
trigger1 = animelem = 6
value = 1,10;210,1
[State 210, 1]
type = PlaySnd
trigger1 = animelem = 4
value = 0,1
[State 610, Helper]
type = Helper
trigger1 = AnimElem = 6
helpertype = normal
name = "Burst"
ID = 611
stateno = 611
pos = 20,-25
postype = p1
facing = 1
[State 210, 2]
type = HitDef
trigger1 = var(6) > 0
trigger1 = time = 0
attr = A, NA
animtype = Med
damage = 36, 0
priority = 5,hit
hitflag = MAF
guardflag = MA
pausetime = 11,11
sparkno = S8010+(random%2)
guard.sparkno = S8030
sparkxy = -5,-45
hitsound = s1,1
guardsound = s2,0
ground.type = High
ground.slidetime = 17
ground.hittime = 20
ground.velocity = -6.5,0
air.velocity = -5,-1
getpower = 60,30
givepower = 30,30
ground.cornerpush.veloff = -6.5
air.cornerpush.veloff = -6.5
id = 610
p2facing = 1
p1facing = 1
nochainid = 3002
[State 1401, TV]
type = targetvelset
trigger1 = movehit = 1
trigger1 = numtarget(610)
trigger1 = target(610),statetype = A
;trigger1 = frontedgebodydist < 140
persistent = 0
ID = 610
x = -12
y = -1.5
[State 1401, TS]
type = targetstate
trigger1 = movehit = 1
trigger1 = numtarget(610)
trigger1 = target(610),statetype = A
;trigger1 = frontedgebodydist < 140
ID = 610
value = 250;650
persistent = 0
ignorehitpause = 1
[State -2, VarA]
type = varadd
trigger1 = movehit = 1
persistent = 0
ignorehitpause = 3
var(6) = -2
[State 610, STS]
type = statetypeset
trigger1 = animelem = 9
physics = A
[State 610, CS]
type = changestate
trigger1 = animtime = 0
value = 50
ctrl = 1
Is it, because of the physics = N from animelem=2 until animelem=9?
Also, I looked up your graze code even further.
I really seems like it's just nothitby which triggers whenever the variable is 1 or 2, plus some additional FX.
I have started to implement that now.