Topology of pathway differences between pathway-tools and .owl file

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Hello, I am using paxtools to parse level 2 and/or 3 .owl files exported from MetaCyc and I've noticed differences between the pathway topology between my parsed output and the view from pathway-tools.

This is one example. I've looked a MetaCyc in version 23.5 for PWY-5733 germacrene biosynthesis. My parsing for the left and right components (getLEFT and getRIGHT in the level 2 parser) and the next reaction step (getNEXT_STEP in level 2-speak) is:

RXN-11527 ReactionStandardName pathwayStep530476
Left component: (2E,6E)-farnesyl diphosphate
Right component: diphosphate
Right component: (+)-germacrene A

RXN-8939 ReactionStandardNamer pathwayStep530477
Left component: (2E,6E)-farnesyl diphosphate
Right component: (+)-germacrene D
Right component: diphosphate
Next step pathwayStep530478
Next step pathwayStep530479
Next step pathwayStep530480

RXN-8562 ReactionStandardName pathwayStep530478
Left component: (2E,6E)-farnesyl diphosphate
Right component: diphosphate
Right component: (-)-germacrene D
Next step pathwayStep530480

RXN-8561 ReactionStandardName pathwayStep530479
Left component: (2E,6E)-farnesyl diphosphate
Right component: germacrene C
Right component: diphosphate
Next step pathwayStep530480

RXN-8553 ReactionStandardName pathwayStep530480
Left component: (2E,6E)-farnesyl diphosphate
Right component: (E,E)-germacrene B
Right component: diphosphate

The information regarding the left and right components of each reaction agrees with the view in pathway-tools. However the next step information links the reactions in a way not otherwise present. My reading of the .owl files confirm that these reactions are linked. Is there a problem in creating the .owl files? Or is my parsing incorrect?