It appears you missed some cpys on the referenced list because Tom had the freeze panel button on, and you probably didn't see them at first.
1	It	it	PRON	PRP	Case=Nom|Gender=Neut|Number=Sing|Person=3|PronType=Prs	2	expl	2:expl	_
2	appears	appear	VERB	VBZ	Mood=Ind|Number=Sing|Person=3|Tense=Pres|VerbForm=Fin	0	root	0:root	_
3	you	you	PRON	PRP	Case=Nom|Person=2|PronType=Prs	4	nsubj	4:nsubj	_
4	missed	miss	VERB	VBD	Mood=Ind|Number=Sing|Person=2|Tense=Past|VerbForm=Fin	2	csubj	2:csubj	_
5	some	some	DET	DT	_	6	det	6:det	_
6	cpys	cpy	NOUN	NNS	Number=Plur	4	obj	4:obj	_
7	on	on	ADP	IN	_	10	case	10:case	_
8	the	the	DET	DT	Definite=Def|PronType=Art	10	det	10:det	_
9	referenced	reference	VERB	VBN	Tense=Past|VerbForm=Part	10	amod	10:amod	_
10	list	list	NOUN	NN	Number=Sing	6	nmod	6:nmod:on	_
11	because	because	SCONJ	IN	_	13	mark	13:mark	_
12	Tom	Tom	PROPN	NNP	Number=Sing	13	nsubj	13:nsubj	_
13	had	have	VERB	VBD	Mood=Ind|Number=Sing|Person=3|Tense=Past|VerbForm=Fin	4	advcl	4:advcl:because	_
14	the	the	DET	DT	Definite=Def|PronType=Art	17	det	17:det	_
15	freeze	freeze	NOUN	NN	Number=Sing	16	compound	16:compound	_
16	panel	panel	NOUN	NN	Number=Sing	17	compound	17:compound	_
17	button	button	NOUN	NN	Number=Sing	13	obj	13:obj|18:nsubj:xsubj	_
18	on	on	ADV	RB	_	13	xcomp	13:xcomp	SpaceAfter=No
19	,	,	PUNCT	,	_	25	punct	25:punct	_
20	and	and	CCONJ	CC	_	25	cc	25:cc	_
21	you	you	PRON	PRP	Case=Nom|Person=2|PronType=Prs	25	nsubj	25:nsubj	_
22	probably	probably	ADV	RB	_	25	advmod	25:advmod	_
23-24	didn't	_	_	_	_	_	_	_	_
23	did	do	AUX	VBD	Mood=Ind|Number=Sing|Person=2|Tense=Past|VerbForm=Fin	25	aux	25:aux	_
24	n't	not	PART	RB	_	25	advmod	25:advmod	_
25	see	see	VERB	VB	VerbForm=Inf	13	conj	4:advcl:because|13:conj:and	_
26	them	they	PRON	PRP	Case=Acc|Number=Plur|Person=3|PronType=Prs	25	obj	25:obj	_
27	at	at	ADP	IN	_	28	case	28:case	_
28	first	first	ADV	RB	NumType=Ord	25	obl	25:obl:at	SpaceAfter=No
29	.	.	PUNCT	.	_	2	punct	2:punct	_
