kubectl top node
is reflecting the actual usage to the VM(nodes), and k8s dashboard is showing the percentage of limit/request you configured.
E.g. Your EC2 instance has 8G memory and you actually use 3237MB so it's 41%. In k8s, you only request 410MB(5.13%), and have a limit of 470MB memory. This doesn't mean you only consume 5.13% memory, but the amount configured.
Namespace Name CPU Requests CPU Limits Memory Requests Memory Limits
--------- ---- ------------ ---------- --------------- -------------
default kube-lego 20m (2%) 0 (0%) 0 (0%) 0 (0%)
default mongo-0 100m (10%) 0 (0%) 0 (0%) 0 (0%)
default web 100m (10%) 0 (0%) 0 (0%) 0 (0%)
kube-system event-exporter- 0 (0%) 0 (0%) 0 (0%) 0 (0%)
kube-system fluentd-gcp-v2.0-z6xh9 100m (10%) 0 (0%) 200Mi (11%) 300Mi (17%)
kube-system heapster-v1.4.0-3405140848-k6cm9 138m (13%) 138m (13%) 301456Ki (17%) 301456Ki (17%)
kube-system kube-dns-3809445927-hn5xk 260m (26%) 0 (0%) 110Mi (6%) 170Mi (9%)
kube-system kube-dns-autoscaler-38801 20m (2%) 0 (0%) 10Mi (0%) 0 (0%)
kube-system kube-proxy-gke-staging-default- 100m (10%) 0 (0%) 0 (0%) 0 (0%)
kube-system kubernetes-dashboard-1962351 100m (10%) 100m (10%) 100Mi (5%) 300Mi (17%)
kube-system l7-default-backend-295440977 10m (1%) 10m (1%) 20Mi (1%) 20Mi (1%)
Here you see many pods with 0 request/limit means unlimited, which didn't count in k8s dashboard but definitely consume memory.
Sum up the memory request/limit you'll find they match k8s dashboard.