Define some point data

In[]:=
pts=
Point data
;​​ListPointPlot3D[pts,ImageSizeMedium]
Out[]=

Get a concave hull mesh

In[]:=
Show[​​concaveHullMesh=ConcaveHullMesh[Most/@pts,115],​​pointPlot=ListPlot[Most/@pts,PlotStyle->Blue]​​]
Out[]=

Corresponding concave hull boundary mesh

In[]:=
Show[​​boundaryMesh=BoundaryMesh[​​concaveHullMesh,​​MeshCellStyle->{{1}->{Thickness@Large,Red},{2}->None}​​],​​pointPlot​​]
Out[]=

Display contour plot

Note : the value of the optional argument MaxPlotPoints is key to constraining contours to lie inside the defined boundary.
In[]:=
rmfun=RegionMember[boundaryMesh]
Out[]=
RegionMemberFunction
Embedding dimension: 2
Region dimension: 2

In[]:=
Manipulate[​​ListContourPlot[​​pts,​​InterpolationOrder->interpolationOrder,​​MaxPlotPoints->maxPlotPoints,​​Mesh->mesh,​​RegionFunction->Function[{x,y,z},rmfun[{x,y}]],​​Epilog->boundaryMesh​​],​​{​​{maxPlotPoints,All},​​Join[{All},Range[2,100,1]],​​ControlType->Slider,​​Appearance->"Labeled"​​},​​{{mesh,All},{All,None}},​​{{interpolationOrder,1},{0,1,2,3}}​​]
Out[]=
​
maxPlotPoints
All
mesh
All
None
interpolationOrder
0
1
2
3
ListContourPlot[pts,InterpolationOrder1,MaxPlotPointsAll,MeshAll,RegionFunctionFunction[{x,y,
z},rmfun[{x,y}]],EpilogboundaryMesh]

What about contouring face-by-face?

Function for scaling BoxRatios

In[]:=
showScaled[g3d_Graphics3D,scaling_List:{1,1,1}]:=​​Module[​​{br},​​br=AbsoluteOptions[g3d,BoxRatios]//First//Values;​​Show[g3d,BoxRatios->br*scaling]​​]​​​​showScaled[mr_MeshRegion,scaling_List:{1,1,1}]:=​​showScaled[​​Show@mr,scaling​​]/;RegionEmbeddingDimension[mr]3​​​​showScaled[scaling_List:{1,1,1}][x_]:=showScaled[x,scaling]

3D mesh region

In[]:=
mr3d=MeshRegion[pts,MeshCells[concaveHullMesh,2]];​​mr3d//showScaled[{1,1,10}]
Out[]=

Get list of all polygons that define the mesh

In[]:=
polys=MeshPrimitives[mr3d,2];​​polys//Short

Range of z coordinate values

Desired contour interval

Contour range

Contour values

ListContourPlot for each mesh cell

Show first to All contoured mesh cells

Show individual mesh cells