A lot of supply-chain communication still runs on EDI: purchase orders, shipping notices, and invoices exchanged with suppliers and 3PLs in a specific structured format. Dynamics 365 can support EDI, but whether a given supplier's EDI setup plugs in cleanly depends entirely on that supplier's own system and how closely it matches what Dynamics expects, which in practice means a fair amount of mapping work per trading partner.
The physical side has its own gap. Barcode scanners, handheld devices, and conveyor or sorting hardware on a warehouse floor often come from a vendor with no native Dynamics connector, which means picks, packs, and shipments either get keyed in after the fact or need a custom bridge between the hardware's own system and Dynamics' inventory records.