Issues you could face are as follows:
1. Constant changes in requirement
(hence try to focus on scalability and accomodation of new requirements in your design phase)
2. Underestimating the requirement for your Server Farm/Data Center
(Sit with your server, storage & DB admins to carefully understand what they require, plan out server farm VLANs, understand etherchannel/channel bonding requirements, check if load balancers are needed, maybe a separate network is required for things like backup inside the prodcution network, this list could go on and still one might miss critical issues)
3. Losing focus on security
(A possiblity especially if you're new, one tends to be too much focused on everything except security. Pay close attention to desiging your enterprise perimeter, if you have sites connected to your office spend time with ISPs to verify your bandwidth requirements, keep business stakeholders aware of security measures which are going to be placed in your network)
4. Test Configuration before implementation day
(test, test and test. keep your configurations ready before implementation day. You don't want to spend too much time figuring out how to connect on the day rather you wanna have ample time to monitor the network behaviour for minor tweakings)
5. Manage stakeholders expectations
Create scope for the project and ensure stakeholders understand what you're trying to achieve. You dont want to hear things later like "our network is sooo slow" or "wireless keeps disconnecting all the time". Agree on the functional capabilities of the network and propose budget accordingly.
As is said "Everthing that can go wrong will go wrong", you can do your best but still miss out. Get in touch with experienced perosnnel like CISCO partners to check your plans/requirements.
